DIAGNOSIS AND TREATMENT OF CANCERS WITH MicroRNA LOCATED IN OR NEAR CANCER-ASSOCIATED CHROMOSOMAL FEATURES

ABSTRACT

MicroRNA genes are highly associated with chromosomal features involved in the etiology of different cancers. The perturbations in the genomic structure or chromosomal architecture of a cell caused by these cancer-associated chromosomal features can affect the expression of the miR gene(s) located in close proximity to that chromosomal feature. Evaluation of miR gene expression can therefore be used to indicate the presence of a cancer-causing chromosomal lesion in a subject. As the change in miR gene expression level caused by a cancer-associated chromosomal feature may also contribute to cancerigenesis, a given cancer can be treated by restoring the level of miR gene expression to normal. microRNA expression profiling can be used to diagnose cancer and predict whether a particular cancer is associated with an adverse prognosis. The identification of specific mutations associated with genomic regions that harbor miR genes in CLL patients provides a means for diagnosing CLL and possibly other cancers.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 11/194,055, filed Jul. 29, 2005, which is a continuation-in-part of International Application No. PCT/US2005/004865, filed Feb. 9, 2005, which claims the benefit of U.S. Provisional Application No. 60/543,119, filed Feb. 9, 2004, U.S. Provisional Application No. 60/542,929, filed Feb. 9, 2004, U.S. Provisional Application No. 60/542,963, filed Feb. 9, 2004, U.S. Provisional Application No. 60/542,940, filed Feb. 9, 2004, U.S. Provisional Application No. 60/580,959, filed Jun. 18, 2004, and U.S. Provisional Application No. 60/580,797, filed Jun. 18, 2004. The entire teachings of the above applications are incorporated herein by reference.

GOVERNMENT SUPPORT

The invention described herein was supported in part by grant nos. P01CA76259, P01CA81534, and P30CA56036 from the National Cancer Institute. The U.S. government has certain rights in this invention

FIELD OF THE INVENTION

The invention relates to the diagnosis of cancers, or the screening of individuals for the predisposition to cancer, by evaluating the status of at least one miR gene located in close proximity to chromosomal features, such as cancer-associated genomic regions, fragile sites, human papilloma virus integration sites, and homeobox genes and gene clusters. The invention also relates to the treatment of cancers by altering the amount of gene product produced from miR genes located in close proximity to these chromosomal features. The invention further provides methods of diagnosing CLL and other cancers by screening for mutations in miR genes.

BACKGROUND OF THE INVENTION

Taken as a whole, cancers are a significant source of mortality and morbidity in the U.S. and throughout the world. However, cancers are a large and varied class of diseases with diverse etiologies. Researchers therefore have been unable to develop treatments or diagnostic tests which cover more than a few types of cancer.

For example, cancers are associated with many different classes of chromosomal features. One such class of chromosomal features are perturbations in the genomic structure of certain genes, such as the deletion or mutation of tumor suppressor genes. The activation of proto-oncogenes by gene amplification or promoter activation (e.g., by viral integration), epigenetic modifications (e.g., a change in DNA methylation) and chromosomal translocations can also cause cancerigenesis. Such perturbations in the genomic structure which are involved in the etiology of cancers are called “cancer-associated genomic regions” or “CAGRs.”

Chromosomal fragile sites are another class of chromosomal feature implicated in the etiology of cancers. Chromosomal fragile sites are regions of genomic DNA which show an abnormally high occurrence of gaps or breaks when DNA synthesis is perturbed during metaphase. These fragile sites are categorized as “rare” or “common.” As their name suggests, rare fragile sites are uncommon. Such sites are associated with di- or tri-nucleotide repeats, can be induced in metaphase chromosomes by folic acid deficiency, and segregate in a Mendelian manner. An exemplary rare fragile site is the Fragile X site.

Common fragile sites are revealed when cells are grown in the presence of aphidocolin or 5-azacytidine, which inhibit DNA polymerase. At least eighty-nine common fragile sites have been identified, and at least one such site is found on every human chromosome. Thus, while their function is poorly understood, common fragile sites represent a basic component of the human chromosome structure.

Induction of fragile sites in vitro leads to increased sister-chromatid exchange and a high rate of chromosomal deletions, amplifications and translocations, while fragile sites have been colocalized with chromosome breakpoints in vivo. Also, most common fragile sites studied in tumor cells contain large, intra-locus deletions or translocations, and a number of tumors have been identified with deletions in multiple fragile sites. Chromosomal fragile sites are therefore mechanistically involved in producing many of the chromosomal lesions commonly seen in cancer cells.

Cervical cancer, which is the second leading cause of female cancer mortality worldwide, is highly associated with human papillomavirus (HPV) infection. Indeed, sequences from the HPV 16 or HPV 18 viruses are found in cells from nearly every cervical tumor cell examined. In malignant forms of cervical cancer, the HPV genome is found integrated into the genome of the cancer cells. HPV preferentially integrates in or near common chromosomal fragile sites. HPV integration into a host cell genome can cause large amplification, deletions or rearrangements near the integration site. Expression of cellular genes near the HPV integration site can therefore be affected, which may contribute to the oncogenesis of the infected cell. These sites of HPV integration into a host cell genome are therefore considered another class of chromosomal feature that is associated with a cancer.

Homeobox genes are a conserved family of regulatory genes that contain the same 183-nucleotide sequence, called the “homeobox.” The homeobox genes encode nuclear transcription factors called “homeoproteins,” which regulate the expression of numerous downstream genes important in development. The homeobox sequence itself encodes a 61 amino acid “homeodomain” that recognizes and binds to a specific DNA binding motif in the target developmental genes. Homeobox genes are categorized as “class I” or “clustered” homeobox genes, which regulate antero-posterior patterning during embryogenesis, or “class II” homeobox genes, which are dispersed throughout the genome. Altogether, the homeobox genes account for more than 0.1% of the vertebrate genome.

The homeobox genes are believed to “decode” external inductive stimuli that signal a given cell to proceed down a particular developmental lineage. For example, specific homeobox genes might be activated in response to various growth factors or other external stimuli that activate signal transduction pathways in a cell. The homeobox genes then activate and/or repress specific programs of effector or developmental genes (e.g., morphogenetic molecules, cell-cycle regulators, pro- or anti-apoptotic proteins, etc.) to induce the phenotype “ordered” by the external stimuli. The homeobox system is clearly highly coordinated during embryogenesis and morphogenesis, but appears to be dysregulated during oncogenesis. Such dysregulation likely occurs because of disruptions in the genomic structure or chromosomal architecture surrounding the homeobox genes or gene clusters. The homeobox genes or gene clusters are therefore considered yet another chromosomal feature which are associated with cancers.

Micro RNAs (miRs) are naturally-occurring 19 to 25 nucleotide transcripts found in over one hundred distinct organisms, including fruit flies, nematodes and humans. The miRs are typically processed from 60- to 70-nucleotide foldback RNA precursor structures, which are transcribed from the miR gene. The miR precursor processing reaction requires Dicer RNase III and Argonaute family members (Sasaki et al. (2003), Genomics 82, 323-330). The miR precursor or processed miR products are easily detected, and an alteration in the levels of these molecules within a cell can indicate a perturbation in the chromosomal region containing the miR gene.

To date, at least 222 separate miR genes have been identified in the human genome. Two miR genes (miR15a and miR16a) have been localized to a homozygously deleted region on chromosome 13 that is correlated with chronic lymphocytic leukemia (Calin et al. (2002), Proc. Natl. Acad. Sci. USA 99:15524-29), and the miR-143/miR145 gene cluster is downregulated in colon cancer (Michael et al. (2003), Mol. Cancer. Res. 1:882-91). However, the distribution of miR genes throughout the genome, and the relationship of the miR genes to the diverse chromosomal features discussed herein, has not been systematically studied.

A method for reliably and accurately diagnosing, or for screening individuals for a predisposition to, cancers associated with such diverse chromosomal features as CAGRs, fragile sites, HPV integration sites and homeobox genes is needed. A method of treating cancers associated with these diverse chromosomal features is also highly desired.

SUMMARY OF THE INVENTION

It has now been discovered that miR genes are commonly associated with chromosomal features involved in the etiology of different cancers. The perturbations in the genomic structure or chromosomal architecture of a cell caused by a cancer-associated chromosomal feature can affect the expression of the miR gene(s) located in close proximity to that chromosomal feature. Evaluation of miR gene expression can therefore be used to indicate the presence of a cancer-causing chromosomal lesion in a subject. As the change in miR gene expression level caused by a cancer-associated chromosomal feature may also contribute to cancerigenesis, a given cancer can be treated by restoring the level of miR gene expression to normal.

The invention therefore provides a method of diagnosing cancer in a subject. The cancer can be any cancer associated with a cancer-associated chromosomal feature. As used herein, a cancer-associated chromosomal feature includes, but is not limited to, a cancer-associated genomic region, a chromosomal fragile site, a human papillomavirus integration site on a chromosome of the subject, and a homeobox gene or gene cluster on a chromosome of the subject. The cancer can also be any cancer associated with one or more adverse prognostic markers, including cancers associated with positive ZAP-70 expression, an unmutated IgV_(H) gene, positive CD38 expression, deletion at chromosome 11q23, and loss or mutation of TP53. In one embodiment, the diagnostic method comprises the following steps. In a sample obtained from a subject suspected of having a cancer associated with a cancer-associated chromosomal feature, the status of at least one miR gene located in close proximity to the cancer-associated chromosomal feature is evaluated by measuring the level of at least one miR gene product from the miR gene in the sample, provided the miR genes are not miR-15, miR-16, miR-143 or miR-145. An alteration in the level of miR gene product in the sample relative to the level of miR gene product in a control sample is indicative of the presence of the cancer in the subject. In a related embodiment, the diagnostic method comprises evaluating in a sample obtained from a subject suspected of having a cancer associated with a cancer-associated chromosomal feature, the status of at least one miR gene located in close proximity to the cancer-associated chromosomal feature, provided the miR gene is not miR-15 or miR-16, by measuring the level of at least one miR gene product from the miR gene in the sample. An alteration in the level of miR gene product in the sample relative to the level of miR gene product in a control sample is indicative of the presence of the cancer in the subject.

The status of the at least one miR gene in the subject's sample can also be evaluated by analyzing the at least one miR gene for a deletion, mutation and/or amplification. The detection of a deletion, mutation and/or amplification in the miR gene relative to the miR gene in a control sample is indicative of the presence of the cancer in the subject. The status of the at least one miR gene in the subject's sample can also be evaluated by measuring the copy number of the at least one miR gene in the sample, wherein a copy number other than two for miR genes located on any chromosome other than a Y chromosome, and other than one for miR genes located on a Y chromosome, is indicative of the subject either having or being at risk for having a cancer. In one embodiment, the diagnostic method comprises analyzing at least one miR gene in the sample for a deletion, mutation and/or amplification, wherein detection of a deletion, mutation and/or amplification in the miR gene relative to the miR gene in a control sample is indicative of the presence of the cancer in the subject. In a related embodiment, the diagnostic method comprises analyzing at least one miR gene in the sample for a deletion, mutation or amplification, provided the miR gene is not miR-15 or miR-16, wherein detection of a deletion, mutation and/or amplification in the miR gene relative to the miR gene in a control sample is indicative of the presence of the cancer in the subject. In a further embodiment, the diagnostic method comprises analyzing the miR-16 gene in the sample for a specific mutation, depicted in SEQ ID NO. 642, wherein detection of the mutation in the miR-16 gene relative to a miR-16 gene in a control sample is indicative of the presence of the cancer in the subject.

The invention also provides a method of screening subjects for a predisposition to develop a cancer associated with a cancer-associated chromosomal feature, by evaluating the status of at least one miR gene located in close proximity to the cancer-associated chromosomal feature in the same manner described herein for the diagnostic method. The cancer can be any cancer associated with a cancer-associated chromosomal feature.

In one embodiment, the level of the at least one miR gene product from the sample is measured by quantitatively reverse transcribing the miR gene product to form a complementary target oligodeoxynucleotide, and hybridizing the target oligodeoxynucleotide to a microarray comprising a probe oligonucleotide specific for the miR gene product. In another embodiment, the levels of multiple miR gene products in a sample are measured in this fashion, by quantitatively reverse transcribing the miR gene products to form complementary target oligodeoxynucleotides, and hybridizing the target oligodeoxynucleotides to a microarray comprising probe oligonucleotides specific for the miR gene products. In another embodiment, the multiple miR gene products are simultaneously reverse transcribed, and the resulting set of target oligodeoxynucleotides are simultaneously exposed to the microarray.

In a related embodiment, the invention provides a method of diagnosing cancer in a subject, comprising reverse transcribing total RNA from a sample from the subject to provide a set of labeled target oligodeoxynucleotides; hybridizing the target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the sample; and comparing the sample hybridization profile to the hybridization profile generated from a control sample, an alteration in the profile being indicative of the subject either having, or being at risk for developing, a cancer. The microarray of miRNA-specific probe oligonucleotides preferably comprises miRNA-specific probe oligonucleotides for a substantial portion of the human miRNome, the full complement of microRNA genes in a cell. The microarray more preferably comprises at least about 60%, 70%, 80%, 90%, or 95% of the human miRNome. In one embodiment, the cancer is associated with a cancer-associated chromosomal feature, such as a cancer-associated genomic region or a chromosomal fragile site. In another embodiment, the cancer is associated with one or more adverse prognostic markers. In a particular embodiment, the cancer is B-cell chronic lymphocytic leukemia. In a further embodiment, the cancer is a subset of B-cell chronic lymphocytic leukemia that is associated with one or more adverse prognostic markers. As used herein, an adverse prognostic marker is any indicator, such as a specific genetic alteration or a level of expression of a gene, whose presence suggests an unfavorable prognosis concerning disease progression, the severity of the cancer, and/or the likelihood of developing the cancer.

The invention further provides a method of treating a cancer associated with a cancer-associated chromosomal feature in a subject. The cancer can be any cancer associated with a cancer-associated chromosomal feature, for example, cancers associated with a cancer-associated genomic region, a chromosomal fragile site, a human papillomavirus integration site on a chromosome of the subject, or a homeobox gene or gene cluster on a chromosome of the subject. Furthermore, the cancer is a cancer associated with a cancer-associated chromosomal feature in which at least one isolated miR gene product from a miR gene located in close proximity to the cancer-associated chromosomal feature is down-regulated or up-regulated in cancer cells of the subject, as compared to control cells. When the at least one isolated miR gene product is down regulated in the subject's cancer cells, the method comprises administering to the subject, an effective amount of at least one isolated miR gene product from the at least one miR gene, such that proliferation of cancer cells in the subject is inhibited. When the at least one isolated miR gene product is up-regulated in the cancer cells, an effective amount of at least one compound for inhibiting expression of the at least one miR gene is administered to the subject, such that proliferation of cancer cells in the subject is inhibited.

The invention further provides a method of treating cancer associated with a cancer-associated chromosomal feature in a subject, comprising the following steps. The amount of miR gene product expressed from at least one miR gene located in close proximity to the cancer-associated chromosomal region in cancer cells from the subject is determined relative to control cells. If the amount of the miR gene product expressed in the cancer cells is less than the amount of the miR gene product expressed in control cells, the amount of miR gene product expressed in the cancer cells is altered by administering to the subject an effective amount of at least one isolated miR gene product from the miR gene, such that proliferation of cancer cells in the subject is inhibited. If the amount of the miR gene product expressed in the cancer cells is greater than the amount of the miR gene product expressed in control cells, the amount of miR gene product expressed in the cancer cells is altered by administering to the subject an effective amount of at least one compound for inhibiting expression of the at least one miR gene, such that proliferation of cancer cells in the subject is inhibited.

The invention further provides pharmaceutical compositions comprising a pharmaceutically acceptable carrier and at least one miR gene product, or a nucleic acid expressing at least one miR gene product, from an miR gene located in close proximity to a cancer-associated chromosomal feature, provided the miR gene product is not miR-15 or miR-16.

The invention still further provides for the use of at least one miR gene product, or a nucleic acid expressing at least one miR gene product, from an miR gene located in close proximity to a cancer-associated chromosomal feature for the manufacture of a medicament for the treatment of a cancer associated with a cancer-associated chromosomal region.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an image of a Northern blot analysis of the expression of miR-16a (upper panel), miR-26a (middle panel), and miR-99a (lower panel) in normal human lung (lane 1) and human lung cancer cells (lanes 2-8). Below the three blots is an image of an ethidium bromide-stained gel indicating the 55 RNA lane loading control. The genomic location and the type of alteration are indicated.

FIG. 2 is a schematic representation demonstrating the position of various miR genes on human chromosomes in relation to HOX gene clusters.

FIG. 3 shows an miRNome expression analysis of 38 individual CLL samples. The main miR-associated CLL clusters are presented. The control samples are: MNC, mononuclear cells; Ly, Diffuse large B cell lymphoma; CD5, selected CD5+ B lymphocytes.

FIG. 4 is an image of a Northern blot analysis of the expression of miR-16a (upper panel), miR-26a (middle panel), and miR-99a (lower panel) in 12 B-CLL samples. Below the three blots is an image of an ethidium bromide-stained gel indicating the 5S RNA lane loading control. miR-16a expression levels varied in these B-CLL cases, and were either low or absent in several of the samples tested. However, the expression levels of miR-26a and miR-99a, both regions not involved in B-CLL, were relatively constant in the tested samples.

FIG. 5 shows Kaplan-Meier curves depicting the relationship between miRNA expression levels and the time from diagnosis to either the time of initial therapy or the present, if therapy had not commenced. The proportion of untreated patients with CLL is plotted against time since diagnosis. The patients are grouped according to the expression profile generated by 11 microRNA genes.

FIG. 6 shows the expression levels of miR-16-1 and miR-15a miRNAs in samples from two patients with a miR-16-1 mutation (see SEQ ID NO. 642) and in CD5+ cell samples from normal patients, both by Northern blot analysis (upper panels) and by miRNACHIP (expression level indicated by numbers below panels).

FIG. 7A is a schematic depicting the locations of mutations affecting various miRNAs. The mutated (below chromosome) and normal (above chromosome) nucleotide base is presented for each mutation/polymorphism. The figure is not drawn to scale.

FIG. 7B depicts the RT-PCR amplification products of primary transcripts corresponding to various mutant miR gene products for which mutations have been identified in B-CLL cells, as well as the length of the amplified genomic DNA (G). GAPDH levels were used for normalization; RT+=reverse transcription, RT−=control without reverse transcription, G=genomic control.

FIG. 7C presents the chromatograms for the genomic regions of samples having either normal miR-16-1/15a (top) or mutated miR-16-1/15a (CtoT)+7 (bottom). The precise position of the precursor (line with period at end) and the location of the mutation (arrowheads) are indicated.

FIG. 7D shows the expression levels by miRNACHIP (MAr) and Northern blot (NB) analysis for miR-16-1 and miR-15a in samples from two normal CD5 pools (CD5+) and from both of the patients carrying the germline (CtoT)+7 mutation (CLL). The Northern blot band intensities were quantified using ImageQuantTL (Nonlinear Dynamics Ltd.). Data are presented as arbitrary units.

FIG. 7E is a Northern blot showing that the germline mutation in the pri-miR-16-1 is associated with abnormal expression of the active, mature miR-16-1 molecule. Levels of expression were assessed in 293 cells transfected with miR-16-1-WT, miR-16-1-MUT or Empty vector (Empty V), as indicated. Untransfected 293 cells were tested as a control. Normalization for loading was performed with a U6 probe (miR-15a; left panel) and the transfection levels were normalized with anti-GFP signal on cell lysates from the same pellet as that used for Northern blotting (miR-16-1; right panel).

DETAILED DESCRIPTION OF THE INVENTION

All nucleic acid sequences herein are given in the 5′ to 3′ direction. In addition, genes are represented by italics, and gene products are represented by normal type; e.g., mir-17 is the gene and miR-17 is the gene product.

It has now been discovered that the genes that comprise the miR gene complement of the human genome (or “miRNome”) are non-randomly distributed throughout the genome in relation to each other. For example, of 222 human miR genes, at least ninety are located in thirty-six gene clusters, typically with two or three miR genes per cluster (median=2.5). The largest cluster is composed of six genes located on chromosome 13 at 13q31; the miR genes in this cluster are miR-17/miR-18/miR-19a/miR-20/miR-19b1/miR-92-1.

The human miR genes are also non-randomly distributed across the human chromosomal complement. For example, chromosome 4 has a less-than-expected rate of miRs, and chromosomes 17 and 19 contain significantly more miR genes than expected based on chromosome size. Indeed, six of the thirty-six miR gene clusters (17%), containing 16 of 90 clustered genes (18%), are located on chromosomes 17 and 19, which account for only 5% of the entire human genome.

The sequences of the gene products of 187 miR genes are provided in Table 1. The location and distribution of these 187 miR genes in the human genome is given in Tables 2 and 3; see also Example 1. All Tables are located in the Examples section below. As used herein, an “miR gene product” or “miRNA” means the unprocessed or processed RNA transcript from an miR gene. As the miR gene products are not translated into a protein, the term “miR gene products” does not include proteins.

A used herein, “probe oligonucleotide” refers to an oligonucleotide that is capable of hybridizing to a target oligonucleotide. “Target oligonucleotide” or “target oligodeoxynucleotide” refers to a molecule to be detected (e.g., in a hybridization). By “miR-specific probe oligonucleotide” or “probe oligonucleotide specific for an miR” is meant a probe oligonucleotide that has a sequence selected to hybridize to a specific miR gene product, or to a reverse transcript of the specific miR gene product.

The unprocessed miR gene transcript is also called an “miR precursor,” and typically comprises an RNA transcript of about 70 nucleotides in length. The miR precursor can be processed by digestion with an RNAse (such as, Dicer, Argonaut, or RNAse III, e.g., E. coli RNAse III)) into an active 19-25 nucleotide RNA molecule. This active 19-25 nucleotide RNA molecule is also called the “processed miR gene transcript.”

The active 19-25 nucleotide RNA molecule can be obtained from the miR precursor through natural processing routes (e.g., using intact cells or cell lysates) or by synthetic processing routes (e.g., using isolated processing enzymes, such as isolated Dicer, Argonaut, or RNAase III). It is understood that the active 19-25 nucleotide RNA molecule can also be produced directly by biological or chemical syntheses, without having been processed from the miR precursor. For ease of discussion, such a directly produced active 19-25 nucleotide RNA molecule is also referred to as a “processed miR gene product.”

As used herein, “miR gene expression” refers to the production of miR gene products from an miR gene, including processing of the miR precursor into a processed miR gene product.

The human miR genes are closely associated with different classes of chromosomal features that are themselves associated with cancer. As used herein, a “cancer-associated chromosomal feature” refers to a region of a given chromosome, which, when perturbed, is correlated with the occurrence of at least one human cancer. As used herein, a chromosomal feature is “correlated” with a cancer when the feature and the cancer occur together in individuals of a study population in a manner not expected on the basis of chance alone.

A region of a chromosome is “perturbed” when the chromosomal architecture or genomic DNA sequence in that region is disturbed or differs from the normal architecture or sequence in that region. Exemplary perturbations of chromosomal regions include, e.g., chromosomal breakage and translocation, mutations, deletions or amplifications of genomic DNA, a change in the methylation pattern of genomic DNA, the presence of fragile sites, and the presence of viral integration sites. One skilled in the art would recognize that other chromosomal perturbations associated with a cancer are possible.

It is understood that a cancer-associated chromosomal feature can be a chromosomal region where perturbations are known to occur at a higher rate than at other regions in the genome, but where the perturbation has not yet occurred. For example, a common chromosomal breakpoint or fragile site is considered a cancer-associated chromosomal feature, even if a break has not yet occurred. Likewise, a region in the genomic DNA known as a mutational “hotspot” can be a cancer-associated chromosomal feature, even if no mutations have yet occurred in the region.

One class of cancer-associated chromosomal feature which is closely associated with miR genes in the human genome is a “cancer-associated genomic region” or “CAGR” (see Table 4). As used herein, a “CAGR” includes any region of the genomic DNA that comprises a genetic or epigenetic change (or the potential for a genetic or epigenetic change) that differs from normal DNA, and which is correlated with a cancer. Exemplary genetic changes include single- and double-stranded breaks (including common breakpoint regions in or near possible oncogenes or tumor-suppressor genes); chromosomal translocations; mutations, deletions, insertions (including viral, plasmid or transposon integrations) and amplifications (including gene duplications) in the DNA; minimal regions of loss-of-heterozygosity (LOH) suggestive of the presence of tumor-suppressor genes; and minimal regions of amplification suggestive of the presence of oncogenes. Exemplary epigenetic changes include any changes in DNA methylation patterns (e.g., DNA hyper- or hypo-methylation, especially in promoter regions). As used herein, “cancer-associated genomic region” or “CAGR” specifically excludes chromosomal fragile sites or human papillomavirus insertion sites.

Many of the known miR genes in the human genome are in or near CAGRs, including 80 miR genes that are located exactly in minimal regions of LOH or minimal regions of amplification correlated to a variety of cancers. Other miR genes are located in or near breakpoint regions, deleted areas, or regions of amplification. The distribution of miR genes in the human genome relative to CAGRs is given in Tables 6 and 7 and in Example 4A below.

As used herein, an miR gene is “associated” with a given CAGR when the miR gene is located in close proximity to the CAGR; i.e., when the miR is located within the same chromosomal band or within 3 megabases (3 Mb) of the CAGR. See Tables 6 and 7 and Example 4A below for a description of cancers which are correlated with CAGRs, and a description of miRs associated with those CAGRs.

For example, cancers associated with CAGRs include leukemia (e.g., AML, CLL, pro-lymphocytic leukemia), lung cancer (e.g., small cell and non-small cell lung carcinoma), esophageal cancer, gastric cancer, colorectal cancer, brain cancer (e.g., astrocytoma, glioma, glioblastoma, medulloblastoma, meningioma, neuroblastoma), bladder cancer, breast cancer, cervical cancer, epithelial cancer, nasopharyngeal cancer (e.g., oral or laryngeal squamous cell carcinoma), lymphoma (e.g., follicular lymphoma), uterine cancer (e.g., malignant fibrous histiocytoma), hepatic cancer (e.g., hepatocellular carcinoma), head-and-neck cancer (e.g., head-and-neck squamous cell carcinoma), renal cancer, male germ cell tumors, malignant mesothelioma, myelodysplastic syndrome, ovarian cancer, pancreatic or biliary cancer, prostate cancer, thyroid cancer (e.g., sporadic follicular thyroid tumors), and urothelial cancer.

Examples of miR genes associated with CAGRs include miR-153-2, let-71, miR-33a, miR-34a-2, miR34a-1, let-7a-1, let-7d; let-7f-1, miR-24-1, miR-27b, miR-23b, miR-181a; miR-199b, miR-218-1, miR-31, let-7a-2, let-7g, miR-21, miR-32a-1, miR-33b, miR-100, miR-101-1, miR-125b-1, miR-135-1, miR-142 as, miR-142s; miR-144, miR-301, miR-297-3, miR-155(BIC), miR-26a, miR-17, miR-18, miR-19a, miR-19b1, miR-20, miR-92-1, miR-128a, miR-7-3, miR-22, miR-123, miR-132, miR-149, miR-161; miR-177, miR-195, miR-212, let-7c, miR-99a, miR-125b-2, miR-210, miR-135-2, miR-124a-1, miR-208, miR-211, miR-180, miR-145, miR-143, miR-127, miR-136, miR-138-1, miR-154, miR-134, miR-299, miR-203, miR-34, miR-92-2, miR-19b-2, miR-108-1, miR-193, miR-106a, miR-29a, miR-29b, miR-129-1, miR-182s, miR-182 as, miR-96, miR-183, miR-32, miR-159-1, miR-192 and combinations thereof.

Specific groupings of miR gene(s) that are associated with a particular cancer are evident from Tables 6 and 7, and are preferred. For example, acute myeloid leukemia (AML) is associated with miR-153-2, and adenocarcinoma of the lung or esophagus is associated with let-71. Where more than one miR gene is listed in Tables 6 and 7, it is understood that the cancer associated with those genes can be diagnosed by evaluating any one of the listed miR genes, or by evaluating any combination of the listed miR genes. Subgenera of CAGRs or associated with miR gene(s) would also be evident to one of ordinary skill in the art from Tables 6 and 7.

Another class of cancer-associated chromosomal feature which is closely associated with miR genes in the human genome is a “chromosomal fragile site” or “FRAs” (see Table 4 and Example 2). As used herein, a “FRA” includes any rare or common fragile site in a chromosome; e.g., one that can be induced by subjecting a cell to stress during DNA replication. For example, a rare FRA can be induced by subjecting the cell to folic acid deficiency during DNA replication. A common FRA can be induced by treating the cell with aphidocolin or 5-azacytidine during DNA replication. The identification or induction of chromosomal fragile sites is within the skill in the art; see, e.g., Arlt et al. (2003), Cytogenet. Genome Res. 100:92-100 and Arlt et al. (2002), Genes, Chromosomes and Cancer 33:82-92, the entire disclosures of which are herein incorporated by reference.

Approximately 20% of the known human miR genes are located in (13 miRs) or within 3 Mb (22 miRs) of cloned FRAs. Indeed, the relative incidence of miR genes inside fragile sites occurs at a rate 9.12 times higher than in non-fragile sites. Moreover, after studying 113 fragile sites in a human karyotype, it was found that 61 miR genes are located in the same chromosomal band as a FRA. The distribution of miR genes in the human genome relative to FRAs is given in Table 5 and in Example 2.

As used herein, an miR gene is “associated” with a given FRA when the miR gene is located in close proximity to the FRA; i.e., when the miR is located within the same chromosomal band or within 3 megabases (3 Mb) of the FRA. See Table 5 and Example 2 for a description of cancers which are correlated with FRAs, and a description of miRs associated with those FRAs.

For example, cancers associated with FRAs include bladder cancer, esophageal cancer, lung cancer, stomach cancer, kidney cancer, cervical cancer, ovarian cancer, breast cancer, lymphoma, Ewing sarcoma, hematopoietic tumors, solid tumors and leukemia.

Examples of miR genes associated with FRAs include miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, miR-175 and combinations thereof.

Specific groupings of miR gene(s) that are associated with a particular cancer and FRA are evident from Table 5, and are preferred. For example, FRA7H is correlated with esophageal cancer, and is associated with miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, and miR-129-1. FRA9D is correlated with bladder cancer, and is associated with let7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, and miR-27b. Where more than one miR gene is listed in Table 5 in association with a FRA, it is understood that the cancer associated with those miR genes can be diagnosed by evaluating any one of the listed miR genes, or by evaluating any combination of the listed miR genes. Subgenera of CAGRs and/or associated with miR gene(s) would also be evident to one of ordinary skill in the art from Table 5.

Another class of cancer-associated chromosomal feature which is closely associated with miR genes in the human genome is a “human papillomavirus (HPV) integration site” (see Table 4 and Example 3). As used herein, an “HPV integration site” includes any site in a chromosome of a subject where some or all of an HPV genome can insert into the genomic DNA, or any site where some or all of an HPV genome has inserted into the genomic DNA. HPV integration sites are often associated with common FRAs, but are distinct from FRAs for purposes of the present invention. Any species or strain of HPV can insert some or all of its genome into an HPV integration site. However, the most common strains of HPV which insert some or all of their genomes into an HPV integration site are HPV 16 and HPV 18. The identification of HPV integration sites in the human genome is within the skill in the art; see, e.g., Thorland et al. (2000), Cancer Res. 60:5916-21, the entire disclosure of which is herein incorporated by reference.

Thirteen miR genes (7%) are located within 2.5 Mb of seven of the seventeen (45%) cloned integration sites in the human genome. The relative incidence of miRs at HPV16 integration sites occurred at a rate 3.22 times higher than in the rest of the genome. Indeed, four miR genes (miR-21, miR-301, miR-142s and miR-142 as) were located within one cluster of integration sites at chromosome 17q23, in which there are three HPV16 integration events spread over roughly 4 Mb of genomic sequence.

As used herein, an miR gene is “associated” with a given HPV integration site when the miR gene is located in close proximity to the HPV integration site; i.e., when the miR is located within the same chromosomal band or within 3 megabases (3 Mb), preferably within 2.5 Mb, of the HPV integration site. See Table 5 and Example 3 for a description of miRs associated with HPV integration sites.

Insertion of HPV sequences into the genome of subject is correlated with the occurrence of cervical cancer. Examples of miR genes associated with HPV integration sites on human chromosomes include miR-21, miR-301, miR-142 as, miR-142s, miR-194, miR-215, miR-32 and combinations thereof.

Specific groupings of miR gene(s) that are associated with a particular HPV integration site are evident from Table 5, and are preferred. For example, the HPV integration site located in or near FRA9E is associated with miR-32. The HPV integration site located in or near FRA1H is associated with miR-194 and miR-215. The HPV integration site located in or near FRA17B is associated with miR-21, miR-301, miR-142s, and miR-142 as. Where more than one miR gene is listed in Table 5 in relation to an HPV integration site, it is understood that the cancer associated with those miR genes can be diagnosed by evaluating any one of the listed miR genes, or by evaluating any combination of the listed miR genes.

Another class of cancer-associated chromosomal feature which is closely associated with miR genes in the human genome is a “homeobox gene or gene cluster” (see Table 4 and Example 5). As used herein, a “homeobox gene or gene cluster” is a single gene or a grouping of genes, characterized in that the gene or genes have been classified by sequence or function as a class I or class II homeobox gene or contain the 183-nucleotide “homeobox” sequence. Identification and characterization of homeobox genes or gene clusters are within the skill in the art; see, e.g., Cillo et al. (1999), Exp. Cell Res. 248:1-9 and Pollard et al. (2000), Current Biology 10:1059-62, the entire disclosures of which are herein incorporated by reference.

Of the four known class I homeobox gene clusters in the human genome, three contain miR genes: miR-10a and miR-196-1 are in the HOX B cluster on 17q21; miR-196-2 is in the HOX C cluster at 12q13; and miR-10b is in the HOX D cluster at 2q31. Three other miRs (miR-148, miR-152 and miR-148b) are located within 1 Mb of a HOX gene cluster. miR genes are also found within class II homeobox gene clusters; for example, seven microRNAs (miR-129-1, miR-153-2, let-7a-1, let-7f-1, let-7d, miR-202 and miR-139) are located within 0.5 Mb of class II homeotic genes. See Example 5 and FIG. 2 for a description of miRs associated with homeobox genes or gene clusters in the human genome.

Examples of homeobox genes associated with miR genes in the human genome include genes in the HOXA cluster, genes in the HOXB cluster, genes in the HOXC cluster, genes in the HOXD cluster, NK1, NK3, NK4, Lbx, Tlx, Emx, Vax, Hmx, NK6, Msx, Cdx, Xlox, Gsx, En, HB9, Gbx, Msx-1, Msx-2, GBX2, HLX, HEX, PMX1, DLX, LHX2 and CDX2. Examples of homeobox gene clusters associated with miR genes in the human genome include HOXA, HOXB, HOXC, HOXD, extended Hox, NKL, ParaHox, and EHGbox, PAX, PBX, MEIS, REIG and PREP/KNOX1.

Examples of cancers associated with homeobox genes or gene clusters include renal cancer, Wilm's tumor, colorectal cancer, small cell lung cancer, melanoma, breast cancer, prostate cancer, skin cancer, osteosarcoma, neuroblastoma, leukemia (acute lymphocytic leukemia, acute myeloid leukemia, chronic lymphocytic leukemia), glioblastoma multiform, medulloblastoma, lymphoplasmacytoid lymphoma, thyroid cancer, rhabdomyosarcoma and solid tumors.

Examples of miR genes associated with homeobox genes or gene clusters include miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, let-7d and combinations thereof.

Specific groupings of miR gene(s) that are associated with particular homeobox genes or gene cluster are evident from Example 5 and FIG. 2, and are preferred. For example, homeobox gene cluster HOXA is associated with miR-148. Homeobox gene cluster HOXB is associated with miR-148, miR-10a, miR-196-1, miR-152 and combinations thereof. Homeobox gene cluster HOXC is associated with miR-196-2, miR-148b or a combination thereof. Homeobox gene cluster HOXD, is associated with miR-10b. Where more than one miR gene is associated with a homeobox gene or gene cluster, it is understood that the cancer associated with those genes can be diagnosed by evaluating any one of the miR genes, or by evaluating any combination of the miR genes. In one embodiment, the miR gene or gene product that is measured or analyzed is not miR-15, miR-16, miR-143 and/or miR-145.

Without wishing to be bound by any theory, it is believed that perturbations in the genomic structure or chromosomal architecture of a cell which comprise the cancer-associated chromosomal feature can affect the expression of the miR gene(s) associated with the feature in that cell. For example, a CAGR can comprise an amplification of the region containing an miR gene(s), causing an up-regulation of miR gene expression. Likewise, the CAGR can comprise a chromosomal breakpoint or a deletion that disrupts gene expression, and results in a down-regulation of miR gene expression. HPV integrations and FRAs can cause deletions, amplifications or rearrangement of the surrounding DNA, which can also affect the structure or expression of any associated miR genes. The factors which cause the collected dysregulation of homeobox genes or gene clusters would cause similar disruptions to any associated miR genes. A change in the status of at least one of the miR genes associated with a cancer-associated chromosomal feature in a tissue or cell sample from a subject, relative to the status of that miR gene in a control sample, therefore is indicative of the presence of a cancer, or a susceptability to cancer, in a subject.

Without wishing to be bound by any theory, it is also believed that a change in status of miR genes associated with a cancer-associated chromosomal feature can be detected prior to, or in the early stages of, the development of transformed or neoplastic phenotypes in cells of a subject. The invention therefore also provides a method of screening subjects for a predisposition to developing a cancer associated with a cancer-associated chromosomal feature, by evaluating the status of at least one miR gene associated with a cancer-associated chromosomal feature in a tissue or cell sample from a subject, relative to the status of that miR gene in a control sample. Subjects with a change in the status of one or more miR genes associated with a cancer-associated chromosomal feature are candidates for further testing to determine or confirm that the subjects have cancer. Such further testing can comprise histological examination of blood or tissue samples, or other techniques within the skill in the art.

As used herein, the “status of an miR gene” refers to the condition of the miR gene in terms of its physical sequence or structure, or its ability to express a gene product. Thus, the status of an miR gene in cells of a subject can be evaluated by any technique suitable for detecting genetic or epigenetic changes in the miR gene, or by any technique suitable for detecting the level of miR gene product produced from the miR gene.

For example, the level of at least one miR gene product produced from an miR gene can be measured in cells of a biological sample obtained from the subject. An alteration in the level (i.e., an up- or down-regulation) of miR gene product in the sample obtained from the subject relative to the level of miR gene product in a control sample is indicative of the presence of the cancer in the subject. As used herein, a “subject” is any mammal suspected of having a cancer associated with a cancer-associated chromosomal feature. In one embodiment, the subject is a human suspected of having a cancer associated with a cancer-associated chromosomal feature. As used herein, expression of an miR gene is “up-regulated” when the amount of miR gene product produced from that gene in a cell or tissue sample from a subject is greater than the amount produced from the same gene in a control cell or tissue sample. Likewise, expression of an miR gene is “down-regulated” when the amount of miR gene product produced from that gene in a cell or tissue sample from a subject is less than the amount produced from the same gene in a control cell or tissue sample.

Methods for determining RNA expression levels in cells from a biological sample are within the level of skill in the art. For example, tissue sample can be removed from a subject suspected of having cancer associated with a cancer-associated chromosomal feature by conventional biopsy techniques. In another example, a blood sample can be removed from the subject, and white blood cells isolated for DNA extraction by standard techniques. The blood or tissue sample is preferably obtained from the subject prior to initiation of radiotherapy, chemotherapy or other therapeutic treatment. A corresponding control tissue or blood sample can be obtained from unaffected tissues of the subject, from a normal human individual or population of normal individuals, or from cultured cells corresponding to the majority of cells in the subject's sample. The control tissue or blood sample is then processed along with the sample from the subject, so that the levels of miR gene product produced from a given miR gene in cells from the subject's sample can be compared to the corresponding miR gene product levels from cells of the control sample.

For example, the relative miR gene expression in the control and normal samples can be conveniently determined with respect to one or more RNA expression standards. The standards can comprise, for example, a zero miR gene expression level, the miR gene expression level in a standard cell line, or the average level of miR gene expression previously obtained for a population of normal human controls.

Suitable techniques for determining the level of RNA transcripts of a particular gene in cells are within the skill in the art. According to one such method, total cellular RNA can be purified from cells by homogenization in the presence of nucleic acid extraction buffer, followed by centrifugation. Nucleic acids are precipitated, and DNA is removed by treatment with DNase and precipitation. The RNA molecules are then separated by gel electrophoresis on agarose gels according to standard techniques, and transferred to nitrocellulose filters by, e.g., the so-called “Northern” blotting technique. The RNA is then immobilized on the filters by heating. Detection and quantification of specific RNA is accomplished using appropriately labeled DNA or RNA probes complementary to the RNA in question. See, for example, Molecular Cloning: A Laboratory Manual, J. Sambrook et al., eds., 2nd edition, Cold Spring Harbor Laboratory Press, 1989, Chapter 7, the entire disclosure of which is incorporated by reference.

Suitable probes for Northern blot hybridization of a given miR gene product can be produced from the nucleic acid sequences provided in Table 1. Methods for preparation of labeled DNA and RNA probes, and the conditions for hybridization thereof to target nucleotide sequences, are described in Molecular Cloning: A Laboratory Manual, J. Sambrook et al., eds., 2nd edition, Cold Spring Harbor Laboratory Press, 1989, Chapters 10 and 11, the disclosures of which are herein incorporated by reference.

For example, the nucleic acid probe can be labeled with, e.g., a radionuclide such as ³H, ³²P, ³³P, ¹⁴C, or ³⁵S; a heavy metal; or a ligand capable of functioning as a specific binding pair member for a labeled ligand (e.g., biotin, avidin or an antibody), a fluorescent molecule, a chemiluminescent molecule, an enzyme or the like.

Probes can be labeled to high specific activity by either the nick translation method of Rigby et al. (1977), J. Mol. Biol. 113:237-251 or by the random priming method of Fienberg et al. (1983), Anal. Biochem. 132:6-13, the entire disclosures of which are herein incorporated by reference. The latter is the method of choice for synthesizing ³²P-labeled probes of high specific activity from single-stranded DNA or from RNA templates. For example, by replacing preexisting nucleotides with highly radioactive nucleotides according to the nick translation method, it is possible to prepare ³²P-labeled nucleic acid probes with a specific activity well in excess of 10⁸ cpm/microgram. Autoradiographic detection of hybridization can then be performed by exposing hybridized filters to photographic film. Densitometric scanning of the photographic films exposed by the hybridized filters provides an accurate measurement of miR gene transcript levels. Using another approach, miR gene transcript levels can be quantified by computerized imaging systems, such the Molecular Dynamics 400-B 2D Phosphorimager available from Amersham Biosciences, Piscataway, N.J.

Where radionuclide labeling of DNA or RNA probes is not practical, the random-primer method can be used to incorporate an analogue, for example, the dTTP analogue 5-(N—(N-biotinyl-epsilon-aminocaproyl)-3-aminoallyl)deoxyuridine triphosphate, into the probe molecule. The biotinylated probe oligonucleotide can be detected by reaction with biotin-binding proteins, such as avidin, streptavidin, and antibodies (e.g., anti-biotin antibodies) coupled to fluorescent dyes or enzymes that produce color reactions.

In addition to Northern and other RNA blotting hybridization techniques, determining the levels of RNA transcripts can be accomplished using the technique of in situ hybridization. This technique requires fewer cells than the Northern blotting technique, and involves depositing whole cells onto a microscope cover slip and probing the nucleic acid content of the cell with a solution containing radioactive or otherwise labeled nucleic acid (e.g., cDNA or RNA) probes. This technique is particularly well-suited for analyzing tissue biopsy samples from subjects. The practice of the in situ hybridization technique is described in more detail in U.S. Pat. No. 5,427,916, the entire disclosure of which is incorporated herein by reference. Suitable probes for in situ hybridization of a given miR gene product can be produced from the nucleic acid sequences provided in Table 1, as described above.

The relative number of miR gene transcripts in cells can also be determined by reverse transcription of miR gene transcripts, followed by amplification of the reverse-transcribed transcripts by polymerase chain reaction (RT-PCR). The levels of miR gene transcripts can be quantified in comparison with an internal standard, for example, the level of mRNA from a “housekeeping” gene present in the same sample. A suitable “housekeeping” gene for use as an internal standard includes, e.g., myosin or glyceraldehyde-3-phosphate dehydrogenase (G3PDH). The methods for quantitative RT-PCR and variations thereof are within the skill in the art.

In some instances, it may be desirable to simultaneously determine the expression level of a plurality of different of miR genes in a sample. In certain instances, it may be desirable to determine the expression level of the transcripts of all known miR genes correlated with cancer. Assessing cancer-specific expression levels for hundreds of miR genes is time consuming and requires a large amount of total RNA (at least 20 μg for each Northern blot) and autoradiographic techniques that require radioactive isotopes. To overcome these limitations, an oligo library in microchip format may be constructed containing a set of probe oligonucleotides specific for a set of miR genes. In one embodiment, the oligo library contains probes corresponding to all known miRs from the human genome. The microchip oligolibrary may be expanded to include additional miRNAs as they are discovered.

The microchip is prepared from gene-specific oligonucleotide probes generated from known miRNAs. According to one embodiment, the array contains two different oligonucleotide probes for each miRNA, one containing the active sequence and the other being specific for the precursor of the miRNA. The array may also contain controls such as one or more mouse sequences differing from human orthologs by only a few bases, which can serve as controls for hybridization stringency conditions. tRNAs from both species may also be printed on the microchip, providing an internal, relatively stable positive control for specific hybridization. One or more appropriate controls for non-specific hybridization may also be included on the microchip. For this purpose, sequences are selected based upon the absence of any homology with any known miRNAs.

The microchip may be fabricated by techniques known in the art. For example, probe oligonucleotides of an appropriate length, e.g., 40 nucleotides, are 5′-amine modified at position C6 and printed using commercially available microarray systems, e.g., the GeneMachine OmniGrid™ 100 Microarrayer and Amersham CodeLink™ activated slides. Labeled cDNA oligomer corresponding to the target RNAs is prepared by reverse transcribing the target RNA with labeled primer. Following first strand synthesis, the RNA/DNA hybrids are denatured to degrade the RNA templates. The labeled target cDNAs thus prepared are then hybridized to the microarray chip under hybridizing conditions, e.g. 6×SSPE/30% formamide at 25° C. for 18 hours, followed by washing in 0.75×TNT at 37° C. for 40 minutes. At positions on the array where the immobilized probe DNA recognizes a complementary target cDNA in the sample, hybridization occurs. The labeled target cDNA marks the exact position on the array where binding occurs, allowing automatic detection and quantification. The output consists of a list of hybridization events, indicating the relative abundance of specific cDNA sequences, and therefore the relative abundance of the corresponding complementary miRs, in the patient sample. According to one embodiment, the labeled cDNA oligomer is a biotin-labeled cDNA, prepared from a biotin-labeled primer. The microarray is then processed by direct detection of the biotin-containing transcripts using, e.g., Streptavidin-Alexa647 conjugate, and scanned utilizing conventional scanning methods. Images intensities of each spot on the array are proportional to the abundance of the corresponding miR in the patient sample.

The use of the array has several advantages for miRNA expression detection. First, the global expression of several hundred genes can be identified in a same sample at one time point. Second, through careful design of the oligonucleotide probes, expression of both mature and precursor molecules can be identified. Third, in comparison with Northern blot analysis, the chip requires a small amount of RNA, and provides reproducible results using 2.5 μg of total RNA. The relatively limited number of miRNAs (a few hundred per species) allows the construction of a common microarray for several species, with distinct oligonucleotide probes for each. Such a tool would allow for analysis of trans-species expression for each known miR under various conditions.

In addition to use for quantitative expression level assays of specific miRs, a microchip containing miRNA-specific probe oligonucleotides corresponding to a substantial portion of the miRNome, preferably the entire miRNome, may be employed to carry out miR gene expression profiling, for analysis of miR expression patterns. Distinct miR signatures may be associated with established disease markers, or directly with a disease state. As described hereinafter in Example 11, two distinct clusters of human B-cell chronic lymphocytic leukemia (CLL) samples are associated with the presence or the absence of Zap-70 expression, a predictor of early disease progression. As described in Examples 11 and 12, two miRNA signatures were associated with the presence of absence of prognostic markers of disease progression, including Zap-70 expression, mutations in the expressed immunoglobulin variable-region gene IgV_(H) and deletions at 13q14. Therefore, miR gene expression profiles can be used for diagnosing the disease state of a cancer, such as whether a cancer is malignant or benign, based on whether or not a given profile is representative of a cancer that is associated with one or more established adverse prognostic markers. Prognostic markers that are suitable for this method include ZAP-70 expression, unmutated IgV_(H) gene, CD38 expression, deletion at chromosome11q23, loss or mutation of TP53, and any combination thereof.

According to the expression profiling method in one embodiment, total RNA from a sample from a subject suspected of having a cancer is quantitatively reverse transcribed to provide a set of labeled target oligodeoxynucleotides complementary to the RNA in the sample. The target oligodeoxynucleotides are then hybridized to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the sample. The result is a hybridization profile for the sample representing the expression pattern of miRNA in the sample. The hybridization profile comprises the signal from the binding of the target oligodeoxynucleotides from the sample to the miRNA-specific probe oligonucleotides in the microarray. The profile may be recorded as the presence or absence of binding (signal vs. zero signal). More preferably, the profile recorded includes the intensity of the signal from each hybridization. The profile is compared to the hybridization profile generated from a normal, i.e., noncancerous, control sample. An alteration in the signal is indicative of the presence of the cancer in the subject.

Other techniques for measuring miR gene expression are also within the skill in the art, and include various techniques for measuring rates of RNA transcription and degradation.

The status of an miR gene in a cell of a subject can also be evaluated by analyzing at least one miR gene or gene product in the sample for a deletion, mutation or amplification, wherein detection of a deletion, mutation or amplification in the miR gene or gene product relative to the miR gene or gene product in a control sample is indicative of the presence of the cancer in the subject. As used herein, a mutation is any alteration in the sequence of a gene of interest that results from one or more nucleotide changes. Such changes include, but are not limited to, allelic polymorphisms, and may affect gene expression and/or function of the gene product.

A deletion, mutation or amplification in an miR gene or gene product can be detected by determining the structure or sequence of an miR gene or gene product in cells from a biological sample from a subject suspected of having cancer associated with a cancer-associated chromosomal feature, and comparing this with the structure or sequence of a corresponding gene or gene product in cells from a control sample. Subject and control samples can be obtained as described herein. Especially suitable candidate miR genes for this type of analysis include, but are not limited to, miR-16-1, miR-27b, miR-206, miR-29b-2 and miR-187. As described in Examples 13 and 14 herein, specific mutations in these five miR genes have been identified in samples from CLL patients.

In certain embodiments, the present invention provides methods for diagnosing whether a subject has, or is at risk for developing, a cancer, comprising analyzing a miR gene or gene product in a test sample from the subject, wherein the detection of a mutation in the miR gene or gene product in the test sample, relative to a control sample, is indicative of the subject having, or being at risk for developing, cancer. In one embodiment, the method comprises analyzing the status of a miR-16-1 gene or gene product. In a particular embodiment, the method comprises analyzing the status of a miR-16-1 gene for the presence of a mutation, wherein the mutation is a C to T nucleotide substitution at +7 base pairs 3′ of the miR-16-1 precursor coding region (see, e.g., SEQ ID NOS:641 and 642). Suitable cancers to be diagnosed by this method include CLL, among others. In another embodiment, the method comprises analyzing the status of a miR-27b gene or gene product. In a particular embodiment, the method comprises analyzing the status of a miR-27b gene for the presence of a mutation, wherein the mutation is a G to A nucleotide substitution at +50 base pairs 3′ of the miR-27b precursor coding region (see, e.g., SEQ ID NOS:645 and 646). Suitable cancers to be diagnosed by this method include, but are not limited to, CLL, throat cancer, and lung cancer. In an additional embodiment, the method comprises analyzing the status of a miR-206 gene or gene product. In a particular embodiment, the method comprises analyzing the status of a miR-206 gene for the presence of a mutation, wherein the mutation is a G to T nucleotide substitution at position 49 of the miR-206 precursor coding region (see, e.g., SEQ ID NOS:657 and 658). In a related embodiment, the method comprises analyzing the status of a miR-206 gene for the presence of a mutation, wherein the mutation is an A to T substitution at −116 base pairs 5′ of the miR-206 precursor coding region (see, e.g., SEQ ID NOS:657 and 659). Suitable cancers to be diagnosed by this method include, but are not limited to, CLL and other leukemias, esophogeal cancer, prostate cancer and breast cancer. In yet another embodiment the method comprises analyzing the status of a miR-29b-2 gene or gene product. In a particular embodiment, the method comprises analyzing the status of a miR-29b-2 gene for the presence of a mutation, wherein the mutation is a G to A nucleotide substitution at +212 base pairs 3′ of the miR-29b-2 precursor coding region (see, e.g., SEQ ID NOS:651 and 652). In a related embodiment, the method comprises analyzing the status of a miR-206 gene for the presence of a mutation, wherein the mutation is an A nucleotide insertion at +107 base pairs 3′ of the miR-29b-2 precursor coding region (see, e.g., SEQ ID NOS:651 and 653). Suitable cancers to be diagnosed by this method include, but are not limited to, CLL and other leukemias, as well as breast cancer. In a further embodiment, the method comprises analyzing the status of a miR-187 gene or gene product. In a particular embodiment, the method comprises analyzing the status of a miR-187 gene for the presence of a mutation, wherein the mutation is a T to C nucleotide substitution at +73 base pairs 3′ of the miR-187 precursor coding region (see, e.g., SEQ ID NOS:654 and 655). Suitable cancers to be diagnosed by this method include, CLL, among others.

Any technique suitable for detecting alterations in the structure or sequence of genes can be used in the practice of the present method. For example, the presence of miR gene deletions, mutations or amplifications can be detected by Southern blot hybridization of the genomic DNA from a subject, using nucleic acid probes specific for miR gene sequences.

Southern blot hybridization techniques are within the skill in the art. For example, genomic DNA isolated from a subject's sample can be digested with restriction endonucleases. This digestion generates restriction fragments of the genomic DNA that can be separated by electrophoresis, for example, on an agarose gel. The restriction fragments are then blotted onto a hybridization membrane (e.g., nitrocellulose or nylon), and hybridized with labeled probes specific for a given miR gene or genes. A deletion or mutation of these genes is indicated by an alteration of the restriction fragment patterns on the hybridization membrane, as compared to DNA from a control sample that has been treated identically to the DNA from the subject's sample. Probe labeling and hybridization conditions suitable for detecting alterations in gene structure or sequence can be readily determined by one of ordinary skill in the art. The miR gene nucleic acid probes for Southern blot hybridization can be designed based upon the nucleic acid sequences provided in Table 1, as described herein. Nucleic acid probe hybridization can then be detected by exposing hybridized filters to photographic film, or by employing computerized imaging systems, such the Molecular Dynamics 400-B 2D Phosphorimager available from Amersham Biosciences, Piscataway, N.J.

Deletions, mutations and/or amplifications of an miR gene can also be detected by amplifying a fragment of these genes by polymerase chain reaction (PCR), and analyzing the amplified fragment by sequencing or by electrophoresis to determine if the sequence and/or length of the amplified fragment from the subject's DNA sample is different from that of a control DNA sample. Suitable reaction and cycling conditions for PCR amplification of DNA fragments can be readily determined by one of ordinary skill in the art.

Deletions of an miR gene can also be identified by detecting deletions of chromosomal markers that are closely linked to the miR gene. Mutations in an miR gene can also be detected by the technique of single strand conformational polymorphism (SSCP), for example, as described in Orita et al. (1989), Genomics 5:874-879 and Hayashi (1991), PCR Methods and Applic. 1:34-38, the entire disclosures of which are herein incorporated by reference. The SSCP technique consists of amplifying a fragment of the gene of interest by PCR; denaturing the fragment and electrophoresing the two denatured single strands under non-denaturing conditions. The single strands assume a complex sequence-dependent intrastrand secondary structure that affects the strands electrophoretic mobility.

The status of an miR gene in cells of a subject can also be evaluated by measuring the copy number of the at least one miR gene in the sample, wherein a gene copy number other than two for miR genes on somatic chromosomes and sex chromosomes in a female, or other than one for miR genes on sex chromosomes in a male, is indicative of the presence of the cancer in the subject.

Any technique suitable for detecting gene copy number can be used in the practice of the present method, including the Southern blot and PCR amplification techniques described above. An alternative method of determining the miR gene copy number in a sample of tissue relies on the fact that many miR genes or gene clusters are closely linked to chromosomal markers or other genes. The loss of a copy of an miR gene in an individual who is heterozygous at a marker or gene closely linked to the miR gene can be inferred from the loss of heterozygosity in the closely linked marker or gene. Methods for determining loss of heterozygosity of chromosomal markers are within the skill in the art.

As discussed above, the human miR genes are closely associated with different classes of chromosomal features that are themselves associated with cancer. These cancers are likely caused, in part, by the perturbation in the chromosome or genomic DNA caused by the cancer-associated chromosomal feature, which can affect expression of oncogenes or tumor-suppressor genes located near the site of perturbation. Without wishing to be bound by any theory, it is believed that the perturbations caused by the cancer-associated chromosomal features also affect the expression level of miR genes associated with the feature, and that this also may also contribute to cancerigenesis. Therefore, a given cancer can be treated by restoring the level of miR gene expression associated with that cancer to normal. For example, if the level of miR gene expression is down-regulated in cancer cells of a subject, then the cancer can be treated by raising the miR expression level. Likewise, if the level of miR gene expression is up-regulated in cancer cells of a subject, then the cancer can be treated by reducing the miR expression level.

The cancers associated with different cancer-associated chromosomal features, and the miR genes associated with these features, are described above and in Tables 5, 6 and 7 and FIG. 2. In the practice of the present method, expression the appropriate miR gene or genes associated with a particular cancer and/or cancer-associated chromosomal features is altered by the compositions and methods described herein. As before, specific groupings of miR gene(s) that are associated with a particular cancer-associated chromosomal feature and/or cancer are evident from Tables 5, 6 and 7 and in FIG. 2, and are preferred. In one embodiment, the method of treatment comprising administering an miR gene product. In another embodiment, the method of treatment comprises administering an miR gene product, provided the miR gene product is not miR-15, miR-16, miR-143 and/or miR-145.

In one embodiment of the present method, the level of at least one miR gene product in cancer cells of a subject is first determined relative to control cells.

Techniques suitable for determining the relative level of miR gene product in cells are described above. If miR gene expression is down-regulated in the cancer cell relative to control cells, then the cancer cells are treated with an effective amount of a compound comprising the isolated miR gene product from the miR gene which is down-regulated. If miR gene expression is up-regulated in cancer cells relative to control cells, then the cancer cells are treated with an effective amount of a compound that inhibits miR gene expression. In one embodiment, the level of miR gene product in a cancer cell is not determined beforehand, for example, in those cancers where miR gene expression is known to be up- or down-regulated.

Thus, in the practice of the present treatment methods, an effective amount of at least one isolated miR gene product can be administered to a subject. As used herein, an “effective amount” of an isolated miR gene product is an amount sufficient to inhibit proliferation of a cancer cell in a subject suffering from a cancer associated with a cancer-associated chromosomal feature. One skilled in the art can readily determine an effective amount of an miR gene product to be administered to a given subject, by taking into account factors such as the size and weight of the subject; the extent of disease penetration; the age, health and sex of the subject; the route of administration; and whether the administration is regional or systemic.

For example, an effective amount of isolated miR gene product can be based on the approximate weight of a tumor mass to be treated. The approximate weight of a tumor mass can be determined by calculating the approximate volume of the mass, wherein one cubic centimeter of volume is roughly equivalent to one gram. An effective amount of the isolated miR gene product based on the weight of a tumor mass can be at least about 10 micrograms/gram of tumor mass, and is preferably between about 10-500 micrograms/gram of tumor mass. More preferably, the effective amount is at least about 60 micrograms/gram of tumor mass. Particularly preferably, the effective amount is at least about 100 micrograms/gram of tumor mass. It is preferred that an effective amount based on the weight of the tumor mass be injected directly into the tumor.

An effective amount of an isolated miR gene product can also be based on the approximate or estimated body weight of a subject to be treated. Preferably, such effective amounts are administered parenterally or enterally, as described herein. For example, an effective amount of the isolated miR gene product is administered to a subject can range from about 5-3000 micrograms/kg of body weight, and is preferably between about 700-1000 micrograms/kg of body weight, and is more preferably greater than about 1000 micrograms/kg of body weight.

One skilled in the art can also readily determine an appropriate dosage regimen for the administration of an isolated miR gene product to a given subject. For example, an miR gene product can be administered to the subject once (e.g., as a single injection or deposition). Alternatively, an miR gene product can be administered once or twice daily to a subject for a period of from about three to about twenty-eight days, more preferably from about seven to about ten days. In a preferred dosage regimen, an miR gene product is administered once a day for seven days. Where a dosage regimen comprises multiple administrations, it is understood that the effective amount of the miR gene product administered to the subject can comprise the total amount of gene product administered over the entire dosage regimen.

As used herein, an “isolated” miR gene product is one which is synthesized, or altered or removed from the natural state through human intervention. For example, an miR gene product naturally present in a living animal is not “isolated.” A synthetic miR gene product, or an miR gene product partially or completely separated from the coexisting materials of its natural state, is “isolated.” An isolated miR gene product can exist in substantially purified form, or can exist in a cell into which the miR gene product has been delivered. Thus, an miR gene product which is deliberately delivered to, or expressed in, a cell is considered an “isolated” miR gene product. An miR gene product produced inside a cell by from an miR precursor molecule is also considered to be “isolated” molecule.

Isolated miR gene products can be obtained using a number of standard techniques. For example, the miR gene products can be chemically synthesized or recombinantly produced using methods known in the art. Preferably, miR gene products are chemically synthesized using appropriately protected ribonucleoside phosphoramidites and a conventional DNA/RNA synthesizer. Commercial suppliers of synthetic RNA molecules or synthesis reagents include, e.g., Proligo (Hamburg, Germany), Dharmacon Research (Lafayette, Colo., USA), Pierce Chemical (part of Perbio Science, Rockford, Ill., USA), Glen Research (Sterling, Va., USA), ChemGenes (Ashland, Mass., USA) and Cruachem (Glasgow, UK).

Alternatively, the miR gene products can be expressed from recombinant circular or linear DNA plasmids using any suitable promoter. Suitable promoters for expressing RNA from a plasmid include, e.g., the U6 or H1 RNA pol III promoter sequences, or the cytomegalovirus promoters. Selection of other suitable promoters is within the skill in the art. The recombinant plasmids of the invention can also comprise inducible or regulatable promoters for expression of the miR gene products in cancer cells.

The miR gene products that are expressed from recombinant plasmids can be isolated from cultured cell expression systems by standard techniques. The miR gene products which are expressed from recombinant plasmids can also be delivered to, and expressed directly in, the cancer cells. The use of recombinant plasmids to deliver the miR gene products to cancer cells is discussed in more detail below.

The miR gene products can be expressed from a separate recombinant plasmid, or can be expressed from the same recombinant plasmid. Preferably, the miR gene products are expressed as the RNA precursor molecules from a single plasmid, and the precursor molecules are processed into the functional miR gene product by a suitable processing system, including processing systems extant within a cancer cell. Other suitable processing systems include, e.g., the in vitro Drosophila cell lysate system as described in U.S. published application 2002/0086356 to Tuschl et al. and the E. coli RNAse III system described in U.S. published patent application 2004/0014113 to Yang et al., the entire disclosures of which are herein incorporated by reference.

Selection of plasmids suitable for expressing the miR gene products, methods for inserting nucleic acid sequences into the plasmid to express the gene products, and methods of delivering the recombinant plasmid to the cells of interest are within the skill in the art. See, for example, Zeng et al. (2002), Molecular Cell 9:1327-1333; Tuschl (2002), Nat. Biotechnol, 20:446-448; Brummelkamp et al. (2002), Science 296:550-553; Miyagishi et al. (2002), Nat. Biotechnol. 20:497-500; Paddison et al. (2002), Genes Dev. 16:948-958; Lee et al. (2002), Nat. Biotechnol. 20:500-505; and Paul et al. (2002), Nat. Biotechnol. 20:505-508, the entire disclosures of which are herein incorporated by reference.

In one embodiment, a plasmid expressing the miR gene products comprises a sequence encoding a miR precursor RNA under the control of the CMV intermediate-early promoter. As used herein, “under the control” of a promoter means that the nucleic acid sequences encoding the miR gene product are located 3′ of the promoter, so that the promoter can initiate transcription of the miR gene product coding sequences.

The miR gene products can also be expressed from recombinant viral vectors. It is contemplated that the miR gene products can be expressed from two separate recombinant viral vectors, or from the same viral vector. The RNA expressed from the recombinant viral vectors can either be isolated from cultured cell expression systems by standard techniques, or can be expressed directly in cancer cells. The use of recombinant viral vectors to deliver the miR gene products to cancer cells is discussed in more detail below.

The recombinant viral vectors of the invention comprise sequences encoding the miR gene products and any suitable promoter for expressing the RNA sequences. Suitable promoters include, for example, the U6 or H1 RNA pol III promoter sequences, or the cytomegalovirus promoters. Selection of other suitable promoters is within the skill in the art. The recombinant viral vectors of the invention can also comprise inducible or regulatable promoters for expression of the miR gene products in a cancer cell.

Any viral vector capable of accepting the coding sequences for the miR gene products can be used; for example, vectors derived from adenovirus (AV); adeno-associated virus (AAV); retroviruses (e.g., lentiviruses (LV), Rhabdoviruses, murine leukemia virus); herpes virus, and the like. The tropism of the viral vectors can be modified by pseudotyping the vectors with envelope proteins or other surface antigens from other viruses, or by substituting different viral capsid proteins, as appropriate.

For example, lentiviral vectors of the invention can be pseudotyped with surface proteins from vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the like. AAV vectors of the invention can be made to target different cells by engineering the vectors to express different capsid protein serotypes. For example, an AAV vector expressing a serotype 2 capsid on a serotype 2 genome is called AAV 2/2. This serotype 2 capsid gene in the AAV 2/2 vector can be replaced by a serotype 5 capsid gene to produce an AAV 2/5 vector. Techniques for constructing AAV vectors which express different capsid protein serotypes are within the skill in the art; see, e.g., Rabinowitz J. E. et al. (2002), J Virol 76:791-801, the entire disclosure of which is herein incorporated by reference.

Selection of recombinant viral vectors suitable for use in the invention, methods for inserting nucleic acid sequences for expressing RNA into the vector, methods of delivering the viral vector to the cells of interest, and recovery of the expressed RNA products are within the skill in the art. See, for example, Dornburg (1995), Gene Therap. 2:301-310; Eglitis (1988), Biotechniques 6:608-614; Miller (1990), Hum. Gene Therap. 1:5-14; and Anderson (1998), Nature 392:25-30, the entire disclosures of which are herein incorporated by reference.

Preferred viral vectors are those derived from AV and AAV. A suitable AV vector for expressing the miR gene products, a method for constructing the recombinant AV vector, and a method for delivering the vector into target cells, are described in Xia et al. (2002), Nat. Biotech. 20:1006-1010, the entire disclosure of which is herein incorporated by reference. Suitable AAV vectors for expressing the miR gene products, methods for constructing the recombinant AAV vector, and methods for delivering the vectors into target cells are described in Samulski et al. (1987), J. Virol. 61:3096-3101; Fisher et al. (1996), J. Virol., 70:520-532; Samulski et al. (1989), J. Virol. 63:3822-3826; U.S. Pat. No. 5,252,479; U.S. Pat. No. 5,139,941; International Patent Application No. WO 94/13788; and International Patent Application No. WO 93/24641, the entire disclosures of which are herein incorporated by reference. Preferably, the miR gene products are expressed from a single recombinant AAV vector comprising the CMV intermediate early promoter.

In one embodiment, a recombinant AAV viral vector of the invention comprises a nucleic acid sequence encoding an miR precursor RNA in operable connection with a polyT termination sequence under the control of a human U6 RNA promoter. As used herein, “in operable connection with a polyT termination sequence” means that the nucleic acid sequences encoding the sense or antisense strands are immediately adjacent to the polyT termination signal in the 5′ direction. During transcription of the miR sequences from the vector, the polyT termination signals act to terminate transcription.

In the practice of the present treatment methods, an effective amount of at least one compound which inhibits miR gene expression can also be administered to the subject. As used herein, “inhibiting miR gene expression” means that the production of miR gene product from the miR gene in the cancer cell after treatment is less than the amount produced prior to treatment. One skilled in the art can readily determine whether miR gene expression has been inhibited in a cancer cell, using for example the techniques for determining miR transcript level discussed above for the diagnostic method.

As used herein, an “effective amount” of a compound that inhibits miR gene expression is an amount sufficient to inhibit proliferation of a cancer cell in a subject suffering from a cancer associated with a cancer-associated chromosomal feature. One skilled in the art can readily determine an effective amount of an miR gene expression-inhibiting compound to be administered to a given subject, by taking into account factors such as the size and weight of the subject; the extent of disease penetration; the age, health and sex of the subject; the route of administration; and whether the administration is regional or systemic.

For example, an effective amount of the expression-inhibiting compound can be based on the approximate weight of a tumor mass to be treated. The approximate weight of a tumor mass can be determined by calculating the approximate volume of the mass, wherein one cubic centimeter of volume is roughly equivalent to one gram. An effective amount based on the weight of a tumor mass can be at least about 10 micrograms/gram of tumor mass, and is preferably between about 10-500 micrograms/gram of tumor mass. More preferably, the effective amount is at least about 60 micrograms/gram of tumor mass. Particularly preferably, the effective amount is at least about 100 micrograms/gram of tumor mass. It is preferred that an effective amount based on the weight of the tumor mass be injected directly into the tumor.

An effective amount of a compound that inhibits miR gene expression can also be based on the approximate or estimated body weight of a subject to be treated. Preferably, such effective amounts are administered parenterally or enterally, as described herein. For example, an effective amount of the expression-inhibiting compound administered to a subject can range from about {tilde over (5)}-3000 micrograms/kg of body weight, and is preferably between about 700-1000 micrograms/kg of body weight, and is more preferably greater than about 1000 micrograms/kg of body weight.

One skilled in the art can also readily determine an appropriate dosage regimen for administering a compound that inhibits miR gene expression to a given subject. For example, an expression-inhibiting compound can be administered to the subject once (e.g., as a single injection or deposition). Alternatively, an expression-inhibiting compound can be administered once or twice daily to a subject for a period of from about three to about twenty-eight days, more preferably from about seven to about ten days. In a preferred dosage regimen, an expression-inhibiting compound is administered once a day for seven days. Where a dosage regimen comprises multiple administrations, it is understood that the effective amount of the expression-inhibiting compound administered to the subject can comprise the total amount of compound administered over the entire dosage regimen.

Suitable compounds for inhibiting miR gene expression include double-stranded RNA (such as short- or small-interfering RNA or “siRNA”), antisense nucleic acids, and enzymatic RNA molecules such as ribozymes. Each of these compounds can be targeted to a given miR gene product and destroy or induce the destruction of the target miR gene product.

For example, expression of a given miR gene can be inhibited by inducing RNA interference of the miR gene with an isolated double-stranded RNA (“dsRNA”) molecule which has at least 90%, for example 95%, 98%, 99% or 100%, sequence homology with at least a portion of the miR gene product. In a preferred embodiment, the dsRNA molecule is a “short or small interfering RNA” or “siRNA.”

siRNA useful in the present methods comprise short double-stranded RNA from about 17 nucleotides to about 29 nucleotides in length, preferably from about 19 to about 25 nucleotides in length. The siRNA comprise a sense RNA strand and a complementary antisense RNA strand annealed together by standard Watson-Crick base-pairing interactions (hereinafter “base-paired”). The sense strand comprises a nucleic acid sequence which is substantially identical to a nucleic acid sequence contained within the target miR gene product.

As used herein, a nucleic acid sequence in an siRNA which is “substantially identical” to a target sequence contained within the target mRNA is a nucleic acid sequence that is identical to the target sequence, or that differs from the target sequence by one or two nucleotides. The sense and antisense strands of the siRNA can comprise two complementary, single-stranded RNA molecules, or can comprise a single molecule in which two complementary portions are base-paired and are covalently linked by a single-stranded “hairpin” area.

The siRNA can also be altered RNA that differs from naturally-occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siRNA or to one or more internal nucleotides of the siRNA, or modifications that make the siRNA resistant to nuclease digestion, or the substitution of one or more nucleotides in the siRNA with deoxyribonucleotides.

One or both strands of the siRNA can also comprise a 3′ overhang. As used herein, a “3′ overhang” refers to at least one unpaired nucleotide extending from the 3′-end of a duplexed RNA strand. Thus, in one embodiment, the siRNA comprises at least one 3′ overhang of from 1 to about 6 nucleotides (which includes ribonucleotides or deoxyribonucleotides) in length, preferably from 1 to about 5 nucleotides in length, more preferably from 1 to about 4 nucleotides in length, and particularly preferably from about 2 to about 4 nucleotides in length. In a preferred embodiment, the 3′ overhang is present on both strands of the siRNA, and is 2 nucleotides in length. For example, each strand of the siRNA can comprise 3′ overhangs of dithymidylic acid (“TT”) or diuridylic acid (“uu”).

The siRNA can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing dsRNA or siRNA molecules are described in U.S. published patent application 2002/0173478 to Gewirtz and in U.S. published patent application 2004/0018176 to Reich et al., the entire disclosures of which are herein incorporated by reference.

Expression of a given miR gene can also be inhibited by an antisense nucleic acid. As used herein, an “antisense nucleic acid” refers to a nucleic acid molecule that binds to target RNA by means of RNA-RNA or RNA-DNA or RNA-peptide nucleic acid interactions, which alters the activity of the target RNA. Antisense nucleic acids suitable for use in the present methods are single-stranded nucleic acids (e.g., RNA, DNA, RNA-DNA chimeras, PNA) that generally comprise a nucleic acid sequence complementary to a contiguous nucleic acid sequence in an miR gene product. Preferably, the antisense nucleic acid comprises a nucleic acid sequence that is 50-100% complementary, more preferably 75-100% complementary, and most preferably 95-100% complementary to a contiguous nucleic acid sequence in an miR gene product. Nucleic acid sequences for the miR gene products are provided in Table 1. Without wishing to be bound by any theory, it is believed that the antisense nucleic acids activate RNase H or some other cellular nuclease that digests the miR gene product/antisense nucleic acid duplex.

Antisense nucleic acids can also contain modifications to the nucleic acid backbone or to the sugar and base moieties (or their equivalent) to enhance target specificity, nuclease resistance, delivery or other properties related to efficacy of the molecule. Such modifications include cholesterol moieties, duplex intercalators such as acridine or the inclusion of one or more nuclease-resistant groups.

Antisense nucleic acids can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing are within the skill in the art; see, e.g., Stein and Cheng (1993), Science 261:1004 and U.S. Pat. No. 5,849,902 to Woolf et al., the entire disclosures of which are herein incorporated by reference.

Expression of a given miR gene can also be inhibited by an enzymatic nucleic acid. As used herein, an “enzymatic nucleic acid” refers to a nucleic acid comprising a substrate binding region that has complementarity to a contiguous nucleic acid sequence of an miR gene product, and which is able to specifically cleave the miR gene product. Preferably, the enzymatic nucleic acid substrate binding region is 50-100% complementary, more preferably 75-100% complementary, and most preferably 95-100% complementary to a contiguous nucleic acid sequence in an miR gene product. The enzymatic nucleic acids can also comprise modifications at the base, sugar, and/or phosphate groups. An exemplary enzymatic nucleic acid for use in the present methods is a ribozyme.

The enzymatic nucleic acids can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing dsRNA or siRNA molecules are described in Werner and Uhlenbeck (1995), Nucl. Acids Res. 23:2092-96; Hammann et al. (1999), Antisense and Nucleic Acid Drug Dev. 9:25-31; and U.S. Pat. No. 4,987,071 to Cech et al, the entire disclosures of which are herein incorporated by reference.

Administration of at least one miR gene product, or at least one compound for inhibiting miR gene expression, will inhibit the proliferation of cancer cells in a subject who has a cancer associated with a cancer-associated chromosomal feature. As used herein, to “inhibit the proliferation of a cancer cell” means to kill the cell, or permanently or temporarily arrest or slow the growth of the cell Inhibition of cancer cell proliferation can be inferred if the number of such cells in the subject remains constant or decreases after administration of the miR gene products or miR gene expression-inhibiting compounds. An inhibition of cancer cell proliferation can also be inferred if the absolute number of such cells increases, but the rate of tumor growth decreases.

The number of cancer cells in a subject's body can be determined by direct measurement, or by estimation from the size of primary or metastatic tumor masses. For example, the number of cancer cells in a subject can be measured by immunohistological methods, flow cytometry, or other techniques designed to detect characteristic surface markers of cancer cells.

The size of a tumor mass can be ascertained by direct visual observation, or by diagnostic imaging methods, such as X-ray, magnetic resonance imaging, ultrasound, and scintigraphy. Diagnostic imaging methods used to ascertain size of the tumor mass can be employed with or without contrast agents, as is known in the art. The size of a tumor mass can also be ascertained by physical means, such as palpation of the tissue mass or measurement of the tissue mass with a measuring instrument, such as a caliper.

The miR gene products or miR gene expression-inhibiting compounds can be administered to a subject by any means suitable for delivering these compounds to cancer cells of the subject. For example, the miR gene products or miR expression inhibiting compounds can be administered by methods suitable to transfect cells of the subject with these compounds, or with nucleic acids comprising sequences encoding these compounds. Preferably, the cells are transfected with a plasmid or viral vector comprising sequences encoding at least one miR gene product or miR gene expression inhibiting compound.

Transfection methods for eukaryotic cells are well known in the art, and include, e.g., direct injection of the nucleic acid into the nucleus or pronucleus of a cell; electroporation; liposome transfer or transfer mediated by lipophilic materials; receptor mediated nucleic acid delivery, bioballistic or particle acceleration; calcium phosphate precipitation, and transfection mediated by viral vectors.

For example, cells can be transfected with a liposomal transfer compound, e.g., DOTAP (N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethyl-ammonium methylsulfate, Boehringer-Mannheim) or an equivalent, such as LIPOFECTIN. The amount of nucleic acid used is not critical to the practice of the invention; acceptable results may be achieved with 0.1-100 micrograms of nucleic acid/10⁵ cells. For example, a ratio of about 0.5 micrograms of plasmid vector in 3 micrograms of DOTAP per 10⁵ cells can be used.

An miR gene product or miR gene expression inhibiting compound can also be administered to a subject by any suitable enteral or parenteral administration route. Suitable enteral administration routes for the present methods include, e.g., oral, rectal, or intranasal delivery. Suitable parenteral administration routes include, e.g., intravascular administration (e.g., intravenous bolus injection, intravenous infusion, intra-arterial bolus injection, intra-arterial infusion and catheter instillation into the vasculature); peri- and intra-tissue injection (e.g., peri-tumoral and intra-tumoral injection, intra-retinal injection, or subretinal injection); subcutaneous injection or deposition, including subcutaneous infusion (such as by osmotic pumps); direct application to the tissue of interest, for example by a catheter or other placement device (e.g., a retinal pellet or a suppository or an implant comprising a porous, non-porous, or gelatinous material); and inhalation. Preferred administration routes are injection, infusion and direct injection into the tumor.

In the present methods, an miR gene product or miR gene expression inhibiting compound can be administered to the subject either as naked RNA, in combination with a delivery reagent, or as a nucleic acid (e.g., a recombinant plasmid or viral vector) comprising sequences that express the miR gene product or expression inhibiting compound. Suitable delivery reagents include, e.g, the Minis Transit TKO lipophilic reagent; lipofectin; lipofectamine; cellfectin; polycations (e.g., polylysine), and liposomes.

Recombinant plasmids and viral vectors comprising sequences that express the miR gene products or miR gene expression inhibiting compounds, and techniques for delivering such plasmids and vectors to cancer cells, are discussed above.

In a preferred embodiment, liposomes are used to deliver an miR gene product or miR gene expression-inhibiting compound (or nucleic acids comprising sequences encoding them) to a subject. Liposomes can also increase the blood half-life of the gene products or nucleic acids.

Liposomes suitable for use in the invention can be formed from standard vesicle-forming lipids, which generally include neutral or negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of factors such as the desired liposome size and half-life of the liposomes in the blood stream. A variety of methods are known for preparing liposomes, for example, as described in Szoka et al. (1980), Ann. Rev. Biophys. Bioeng. 9:467; and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369, the entire disclosures of which are herein incorporated by reference.

The liposomes for use in the present methods can comprise a ligand molecule that targets the liposome to cancer cells. Ligands which bind to receptors prevalent in cancer cells, such as monoclonal antibodies that bind to tumor cell antigens, are preferred.

The liposomes for use in the present methods can also be modified so as to avoid clearance by the mononuclear macrophage system (“MMS”) and reticuloendothelial system (“RES”). Such modified liposomes have opsonization-inhibition moieties on the surface or incorporated into the liposome structure. In a particularly preferred embodiment, a liposome of the invention can comprise both opsonization-inhibition moieties and a ligand.

Opsonization-inhibiting moieties for use in preparing the liposomes of the invention are typically large hydrophilic polymers that are bound to the liposome membrane. As used herein, an opsonization inhibiting moiety is “bound” to a liposome membrane when it is chemically or physically attached to the membrane, e.g., by the intercalation of a lipid-soluble anchor into the membrane itself, or by binding directly to active groups of membrane lipids. These opsonization-inhibiting hydrophilic polymers form a protective surface layer that significantly decreases the uptake of the liposomes by the MMS and RES; e.g., as described in U.S. Pat. No. 4,920,016, the entire disclosure of which is herein incorporated by reference.

Opsonization inhibiting moieties suitable for modifying liposomes are preferably water-soluble polymers with a number-average molecular weight from about 500 to about 40,000 daltons, and more preferably from about 2,000 to about 20,000 daltons. Such polymers include polyethylene glycol (PEG) or polypropylene glycol (PPG) derivatives; e.g., methoxy PEG or PPG, and PEG or PPG stearate; synthetic polymers such as polyacrylamide or poly N-vinyl pyrrolidone; linear, branched, or dendrimeric polyamidoamines; polyacrylic acids; polyalcohols, e.g., polyvinylalcohol and polyxylitol to which carboxylic or amino groups are chemically linked, as well as gangliosides, such as ganglioside GM1. Copolymers of PEG, methoxy PEG, or methoxy PPG, or derivatives thereof, are also suitable. In addition, the opsonization inhibiting polymer can be a block copolymer of PEG and either a polyamino acid, polysaccharide, polyamidoamine, polyethyleneamine, or polynucleotide. The opsonization inhibiting polymers can also be natural polysaccharides containing amino acids or carboxylic acids, e.g., galacturonic acid, glucuronic acid, mannuronic acid, hyaluronic acid, pectic acid, neuraminic acid, alginic acid, carrageenan; aminated polysaccharides or oligosaccharides (linear or branched); or carboxylated polysaccharides or oligosaccharides, e.g., reacted with derivatives of carbonic acids with resultant linking of carboxylic groups. Preferably, the opsonization-inhibiting moiety is a PEG, PPG, or derivatives thereof. Liposomes modified with PEG or PEG-derivatives are sometimes called “PEGylated liposomes.”

The opsonization inhibiting moiety can be bound to the liposome membrane by any one of numerous well-known techniques. For example, an N-hydroxysuccinimide ester of PEG can be bound to a phosphatidyl-ethanolamine lipid-soluble anchor, and then bound to a membrane. Similarly, a dextran polymer can be derivatized with a stearylamine lipid-soluble anchor via reductive amination using Na(CN)BH₃ and a solvent mixture, such as tetrahydrofuran and water in a 30:12 ratio at 60° C.

Liposomes modified with opsonization-inhibition moieties remain in the circulation much longer than unmodified liposomes. For this reason, such liposomes are sometimes called “stealth” liposomes. Stealth liposomes are known to accumulate in tissues fed by porous or “leaky” microvasculature. Thus, tissue characterized by such microvasculature defects, for example solid tumors, will efficiently accumulate these liposomes; see Gabizon, et al. (1988), Proc. Natl. Acad. Sci., USA, 18:6949-53. In addition, the reduced uptake by the RES lowers the toxicity of stealth liposomes by preventing significant accumulation of the liposomes in the liver and spleen. Thus, liposomes that are modified with opsonization-inhibition moieties are particularly suited to deliver the miR gene products or miR gene expression inhibition compounds (or nucleic acids comprising sequences encoding them) to tumor cells.

The miR gene products or miR gene expression inhibition compounds are preferably formulated as pharmaceutical compositions, sometimes called “medicaments,” prior to administering to a subject, according to techniques known in the art. Pharmaceutical compositions of the present invention are characterized as being at least sterile and pyrogen-free. As used herein, “pharmaceutical formulations” include formulations for human and veterinary use. Methods for preparing pharmaceutical compositions of the invention are within the skill in the art, for example as described in Remington's Pharmaceutical Science, 17th ed., Mack Publishing Company, Easton, Pa. (1985), the entire disclosure of which is herein incorporated by reference.

The present pharmaceutical formulations comprise at least one miR gene product or miR gene expression inhibition compound (or at least one nucleic acid comprising sequences encoding them) (e.g., 0.1 to 90% by weight), or a physiologically acceptable salt thereof, mixed with a pharmaceutically-acceptable carrier. The pharmaceutical formulations of the invention can also comprise at least one miR gene product or miR gene expression inhibition compound (or at least one nucleic acid comprising sequences encoding them) which are encapsulated by liposomes and a pharmaceutically-acceptable carrier. In one embodiment, the pharmaceutical compositions comprise an miR gene or gene product that is not miR-15, miR-16, miR-143 and/or miR-145.

Preferred pharmaceutically-acceptable carriers are water, buffered water, normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid and the like.

In a preferred embodiment, the pharmaceutical compositions of the invention comprise at least one miR gene product or miR gene expression inhibition compound (or at least one nucleic acid comprising sequences encoding them) which is resistant to degradation by nucleases. One skilled in the art can readily synthesize nucleic acids which are nuclease resistant, for example by incorporating one or more ribonucleotides that are modified at the 2′-position into the miR gene products. Suitable 2′-modified ribonucleotides include those modified at the 2′-position with fluoro, amino, alkyl, alkoxy, and O-allyl.

Pharmaceutical compositions of the invention can also comprise conventional pharmaceutical excipients and/or additives. Suitable pharmaceutical excipients include stabilizers, antioxidants, osmolality adjusting agents, buffers, and pH adjusting agents. Suitable additives include, e.g., physiologically bio compatible buffers (e.g., tromethamine hydrochloride), additions of chelants (such as, for example, DTPA or DTPA-bisamide) or calcium chelate complexes (such as, for example, calcium DTPA, CaNaDTPA-bisamide), or, optionally, additions of calcium or sodium salts (for example, calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate). Pharmaceutical compositions of the invention can be packaged for use in liquid form, or can be lyophilized.

For solid pharmaceutical compositions of the invention, conventional nontoxic solid pharmaceutically-acceptable carriers can be used; for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.

For example, a solid pharmaceutical composition for oral administration can comprise any of the carriers and excipients listed above and 10-95%, preferably 25%-75%, of the at least one miR gene product or miR gene expression inhibition compound (or at least one nucleic acid comprising sequences encoding them). A pharmaceutical composition for aerosol (inhalational) administration can comprise 0.01-20% by weight, preferably 1%-10% by weight, of the at least one miR gene product or miR gene expression inhibition compound (or at least one nucleic acid comprising sequences encoding them) encapsulated in a liposome as described above, and a propellant. A carrier can also be included as desired; e.g., lecithin for intranasal delivery.

The invention will now be illustrated by the following non-limiting examples.

EXAMPLES

The following techniques were used in the Examples.

General Methods:

The miR gene database

A set of 187 human miR genes was compiled (see Table 1). The set comprises 153 miRs identified in the miR Registry (maintained by the Wellcome Trust Sanger Institute, Cambridge, UK), and 36 other miRs manually curated from published papers (Lim et al., 2003, Science 299:1540; Lagos-Quintana et al., 2001, Science 294:853-858; Lau et al., 2001, Science 294:858-862; Lee et al., 2001, Science 294:862-864; Mourelatos et al., 2002, Genes Dev. 16:720-728; Lagos-Quintana et al., 2002, Curr. Biol. 12:735-739; Dostie et al., 2003, RNA 9:180-186; Houbaviy et al., 2003, Dev. Cell. 5:351-8) or found in the GenBank database accessed through the National Center for Biotechnology Information (NCBI) website, maintained by the National Institutes of Health and the National Library of Medicine Nineteen new human miRs (approximately 10% of the miR set) were found based on their homology with cloned miRs from other species (mainly mouse). For all miRs, the sequence of the precursor was identified using the M Zucker RNA folding program and selecting the precursor sequence that gave the best score for the hairpin structure. The program is available and is maintained by Michael Zucker of Rensselaer Polytechnic Institute.

TABLE 1 Human miR Gene Product Sequences SEQ ID Name Precursor Sequence (5′ to 3′)* NO. has-let-7a-l-prec CACTGTGGGATGAGGTAGTAGGTTGTATAGTTTTAGG 1 GTCACACCCACCACTGGGAGATAACTATACAATCTAC TGTCTTTCCTAACGTG hsa-let-7a-2-prec AGGTTGAGGTAGTAGGTTGTATAGTTTAGAATTACAT 2 CAAGGGAGATAACTGTACAGCCTCCTAGCTTTCCT hsa-let-7a-3-prec GGGTGAGGTAGTAGGTTGTATAGT TTGGGGCTCTGCC 3 CTGCTATGGGATAACTATACAATCTACTGTCTTTCCT hsa-let-7a-4-prec GTGACTGCATGCTCCCAGGTTGAGGTAGTAGGTTGTA 4 TAGTTTAGAATTACACAAGGGAGATAACTGTACAGCC TCCTAGCTTTCCTTGGGTCTTGCACTAAACAAC hsa-let-7b-prec GGCGGGGTGAGGTAGTAGGTTGTGTGGTTTCAGGGCA 5 GTGATGTTGCCCCTCGGAAGATAACTATACAACCTAC TGCCTTCCCTG hsa-let-7c-prec GCATCCGGGTTGAGGTAGTAGGTTGTATGGTTTAGAG 6 TTACACCCTGGGAGTTAACTGTACAACCTTCTAGCTTT CCTTGGAGC hsa-let-7d-prec CCTAGGAAGAGGTAGTAGGTTGCATAGTTTTAGGGCA 7 GGGATTTTGCCCACAAGGAGGTAACTATACGACCTGC TGCCTTTCTTAGG hsa-let-7d-v1-prec CTAGGAAGAGGTAGTAGTTTGCATAGTTTTAGGGCAA 8 AGATTTTGCCCACAAGTAGTTAGCTATACGACCTGCA GCCTTTTGTAG hsa-let-7d-v2-prec CTGGCTGAGGTAGTAGTTTGTGCTGTTGGTCGGGTTGT 9 GACATTGCCCGCTGTGGAGATAACTGCGCAAGCTACT GCCTTGCTAG hsa-let-7e-prec CCCGGGCTGAGGTAGGAGGTTGTATAGTTGAGGAGGA 10 CACCCAAGGAGATCACTATACGGCCTCCTAGCTTTCCC CAGG hsa-let-7f-1-prec TCAGAGTGAGGTAGTAGATTGTATAGTTGTGGGGTAG 11 TGATTTTACCCTGTTCAGGAGATAACTATACAATCTAT TGCCTTCCCTGA hsa-let-7f-2-prec CTGTGGGATGAGGTAGTAGATTGTATAGTTGTGGGGT 12 AGTGATTTTACCCTGTTCAGGAGATAACTATACAATCT ATTGCCTTCCCTGA hsa-let-7f-2-prec CTGTGGGATGAGGTAGTAGATTGTATAGTTTTAGGGT 13 CATACCCCATCTTGGAGATAACTATACAGTCTACTGTC TTTCCCACGG hsa-let-7g-prec TTGCCTGATTCCAGGCTGAGGTAGTAGTTTGTACAGTT 14 TGAGGGTCTATGATACCACCCGGTACAGGAGATAACT GTACAGGCCACTGCCTTGCCAGGAACAGCGCGC hsa-let-7i-prec CTGGCTGAGGTAGTAGTTTGTGCTGTTGGTCGGGTTGT 15 GACATTGCCCGCTGTGGAGATAACTGCGCAAGCTACT GCCTTGCTAG hsa-mir-001b-1- ACCTACTCAGAGTACATACTTCTTTATGTACCCATATG 16 prec AACATACAATGCTATGGAATGTAAAGAAGTATGTATT TTTGGTAGGC hsa-mir-001b-1- CAGCTAACAACTTAGTAATACCTACTCAGAGTACATA 17 prec CTTCTTTATGTACCCATATGAACATACAATGCTATGGA ATGTAAAGAAGTATGTATTTTTGGTAGGCAATA hsa-mir-001b-2- GCCTGCTTGGGAAACATACTTCTTTATATGCCCATATG 18 prec GACCTGCTAAGCTATGGAATGTAAAGAAGTATGTATC TCAGGCCGGG hsa-mir-001b- TGGGAAACATACTTCTTTATATGCCCATATGGACCTGC 19 prec TAAGCTATGGAATGTAAAGAAGTATGTATCTCA hsa-mir-001d- ACCTACTCAGAGTACATACTTCTTTATGTACCCATATG 20 prec AACATACAATGCTATGGAATGTAAAGAAGTATGTATT TTTGGTAGGC hsa-mir-007-1 TGGATGTTGGCCTAGTTCTGTGTGGAAGACTAGTGATT 21 TTGTTGTTTTTAGATAACTAAATCGACAACAAATCACA GTCTGCCATATGGCACAGGCCATGCCTCTACA hsa-mir-007-1- TTGGATGTTGGCCTAGTTCTGTGTGGAAGACTAGTGAT 22 prec TTTGTTGTTTTTAGATAACTAAATCGACAACAAATCAC AGTCTGCCATATGGCACAGGCCATGCCTCTACAG hsa-mir-007-2 CTGGATACAGAGTGGACCGGCTGGCCCCATCTGGAAG 23 ACTAGTGATTTTGTTGTTGTCTTACTGCGCTCAACAAC AAATCCCAGTCTACCTAATGGTGCCAGCCATCGCA hsa-mir-007-2- CTGGATACAGAGTGGACCGGCTGGCCCCATCTGGAAG 24 prec ACTAGTGATTTTGTTGTTGTCTTACTGCGCTCAACAAC AAATCCCAGTCTACCTAATGGTGCCAGCCATCGCA hsa-mir-007-3 AGATTAGAGTGGCTGTGGTCTAGTGCTGTGTGGAAGA 25 CTAGTGATTTTGTTGTTCTGATGTACTACGACAACAAG TCACAGCCGGCCTCATAGCGCAGACTCCCTTCGAC hsa-mir-007-3- AGATTAGAGTGGCTGTGGTCTAGTGCTGTGTGGAAGA 26 prec CTAGTGATTTTGTTGTTCTGATGTACTACGACAACAAG TCACAGCCGGCCTCATAGCGCAGACTCCCTTCGAC hsa-mir-009-1 CGGGGTTGGTTGTTATCTTTGGTTATCTAGCTGTATGA 27 GTGGTGTGGAGTCTTCATAAAGCTAGATAACCGAAAG TAAAAATAACCCCA hsa-mir-009-2 GGAAGCGAGTTGTTATCTTTGGTTATCTAGCTGTATGA 28 GTGTATTGGTCTTCATAAAGCTAGATAACCGAAAGTA AAAACTCCTTCA hsa-mir-009-3 GGAGGCCCGTTTCTCTCTTTGGTTATCTAGCTGTATGA 29 GTGCCACAGAGCCGTCATAAAGCTAGATAACCGAAAG TAGAAATGATTCTCA hsa-mir-010a-prec GATCTGTCTGTCTTCTGTATATACCCTGTAGATCCGAA 30 TTTGTGTAAGGAATTTTGTGGTCACAAATTCGTATCTA GGGGAATATGTAGTTGACATAAACACTCCGCTCT hsa-mir-010b- CCAGAGGTTGTAACGTTGTCTATATATACCCTGTAGAA 31 prec CCGAATTTGTGTGGTATCCGTATAGTCACAGATTCGAT TCTAGGGGAATATATGGTCGATGCAAAAACTTCA hsa-mir-015a-2- GCGCGAATGTGTGTTTAAAAAAAATAAAACCTTGGAG 32 prec TAAAGTAGCAGCACATAATGGTTTGTGGATTTTGAAA AGGTGCAGGCCATATTGTGCTGCCTCAAAAATAC hsa-mir-015a-prec CCTTGGAGTAAAGTAGCAGCACATAATGGTTTGTGGA 33 TTTTGAAAAGGTGCAGGCCATATTGTGCTGCCTCAAA AATACAAGG hsa-mir-015b- CTGTAGCAGCACATCATGGTTTACATGCTACAGTCAA 34 prec GATGCGAATCATTATTTGCTGCTCTAG hsa-mir-015b- TTGAGGCCTTAAAGTACTGTAGCAGCACATCATGGTTT 35 prec ACATGCTACAGTCAAGATGCGAATCATTATTTGCTGCT CTAGAAATTTAAGGAAATTCAT hsa-mir-016a- GTCAGCAGTGCCTTAGCAGCACGTAAATATTGGCGTT 36 chr13 AAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCT GAAGTAAGGTTGAC hsa-mir-016b- GTTCCACTCTAGCAGCACGTAAATATTGGCGTAGTGA 37 chr3 AATATATATTAAACACCAATATTACTGTGCTGCTTTAG TGTGAC hsa-mir-016-prec- GCAGTGCCTTAGCAGCACGTAAATATTGGCGTTAAGA 38 13 TTCTAAAATTATCTCCAGTATTAACTGTGCTGCTGAAG TAAGGT hsa-mir-017-prec GTCAGAATAATGTCAAAGTGCTTACAGTGCAGGTAGT 39 GATATGTGCATCTACTGCAGTGAAGGCACTTGTAGCA TTATGGTGAC hsa-mir-018-prec TGTTCTAAGGTGCATCTAGTGCAGATAGTGAAGTAGA 40 TTAGCATCTACTGCCCTAAGTGCTCCTTCTGGCA hsa-mir-018-prec- TTTTTGTTCTAAGGTGCATCTAGTGCAGATAGTGAAGT 41 13 AGATTAGCATCTACTGCCCTAAGTGCTCCTTCTGGCAT AAGAA hsa-mir-019a-prec GCAGTCCTCTGTTAGTTTTGCATAGTTGCACTACAAGA 42 AGAATGTAGTTGTGCAAATCTATGCAAAACTGATGGT GGCCTGC hsa-mir-019a- CAGTCCTCTGTTAGTTTTGCATAGTTGCACTACAAGAA 43 prec-13 GAATGTAGTTGTGCAAATCTATGCAAAACTGATGGTG GCCTG hsa-mir-019b-1- CACTGTTCTATGGTTAGTTTTGCAGGTTTGCATCCAGC 44 prec TGTGTGATATTCTGCTGTGCAAATCCATGCAAAACTGA CTGTGGTAGTG hsa-mir-019b-2- ACATTGCTACTTACAATTAGTTTTGCAGGTTTGCATTT 45 prec CAGCGTATATATGTATATGTGGCTGTGCAAATCCATGC AAAACTGATTGTGATAATGT hsa-mir-019b- TTCTATGGTTAGTTTTGCAGGTTTGCATCCAGCTGTGT 46 prec-13 GATATTCTGCTGTGCAAATCCATGCAAAACTGACTGT GGTAG hsa-mir-019b- TTACAATTAGTTTTGCAGGTTTGCATTTCAGCGTATAT 47 prec-X ATGTATATGTGGCTGTGCAAATCCATGCAAAACTGAT TGTGAT hsa-mir-020-prec GTAGCACTAAAGTGCTTATAGTGCAGGTAGTGTTTAG 48 TTATCTACTGCATTATGAGCACTTAAAGTACTGC hsa-mir-021-prec TGTCGGGTAGCTTATCAGACTGATGTTGACTGTTGAAT 49 CTCATGGCAACACCAGTCGATGGGCTGTCTGACA hsa-mir-021-prec- ACCTTGTCGGGTAGCTTATCAGACTGATGTTGACTGTT 50 17 GAATCTCATGGCAACACCAGTCGATGGGCTGTCTGAC ATTTTG hsa-mir-022-prec GGCTGAGCCGCAGTAGTTCTTCAGTGGCAAGCTTTAT 51 GTCCTGACCCAGCTAAAGCTGCCAGTTGAAGAACTGT TGCCCTCTGCC hsa-mir-023a-prec GGCCGGCTGGGGTTCCTGGGGATGGGATTTGCTTCCT 52 GTCACAAATCACATTGCCAGGGATTTCCAACCGACC hsa-mir-023b- CTCAGGTGCTCTGGCTGCTTGGGTTCCTGGCATGCTGA 53 prec TTTGTGACTTAAGATTAAAATCACATTGCCAGGGATTA CCACGCAACCACGACCTTGGC hsa-mir-023-prec- CCACGGCCGGCTGGGGTTCCTGGGGATGGGATTTGCT 54 19 TCCTGTCACAAATCACATTGCCAGGGATTTCCAACCG ACCCTGA hsa-mir-024-1- CTCCGGTGCCTACTGAGCTGATATCAGTTCTCATTTTA 55 prec CACACTGGCTCAGTTCAGCAGGAACAGGAG hsa-mir-024-2- CTCTGCCTCCCGTGCCTACTGAGCTGAAACACAGTTGG 56 prec TTTGTGTACACTGGCTCAGTTCAGCAGGAACAGGG hsa-mir-024-prec- CCCTGGGCTCTGCCTCCCGTGCCTACTGAGCTGAAACA 57 19 CAGTTGGTTTGTGTACACTGGCTCAGTTCAGCAGGAA CAGGGG hsa-mir-024-prec- CCCTCCGGTGCCTACTGAGCTGATATCAGTTCTCATTT 58 9 TACACACTGGCTCAGTTCAGCAGGAACAGCATC hsa-mir-025-prec GGCCAGTGTTGAGAGGCGGAGACTTGGGCAATTGCTG 59 GACGCTGCCCTGGGCATTGCACTTGTCTCGGTCTGACA GTGCCGGCC hsa-mir-026a-prec AGGCCGTGGCCTCGTTCAAGTAATCCAGGATAGGCTG 60 TGCAGGTCCCAATGGCCTATCTTGGTTACTTGCACGGG GACGCGGGCCT hsa-mir-026b- CCGGGACCCAGTTCAAGTAATTCAGGATAGGTTGTGT 61 prec GCTGTCCAGCCTGTTCTCCATTACTTGGCTCGGGGACC GG hsa-mir-027a-prec CTGAGGAGCAGGGCTTAGCTGCTTGTGAGCAGGGTCC 62 ACACCAAGTCGTGTTCACAGTGGCTAAGTTCCGCCCC CCAG hsa-mir-027b- AGGTGCAGAGCTTAGCTGATTGGTGAACAGTGATTGG 63 prec TTTCCGCTTTGTTCACAGTGGCTAAGTTCTGCACCT hsa-mir-027b- ACCTCTCTAACAAGGTGCAGAGCTTAGCTGATTGGTG 64 prec AACAGTGATTGGTTTCCGCTTTGTTCACAGTGGCTAAG TTCTGCACCTGAAGAGAAGGTG hsa-mir-027-prec- CCTGAGGAGCAGGGCTTAGCTGCTTGTGAGCAGGGTC 65 19 CACACCAAGTCGTGTTCACAGTGGCTAAGTTCCGCCC CCCAGG hsa-mir-028-prec GGTCCTTGCCCTCAAGGAGCTCACAGTCTATTGAGTTA 66 CCTTTCTGACTTTCCCACTAGATTGTGAGCTCCTGGAG GGCAGGCACT hsa-mir-029a-2 CCTTCTGTGACCCCTTAGAGGATGACTGATTTCTTTTG 67 GTGTTCAGAGTCAATATAATTTTCTAGCACCATCTGAA ATCGGTTATAATGATTGGGGAAGAGCACCATG hsa-mir-029a-prec ATGACTGATTTCTTTTGGTGTTCAGAGTCAATATAATT 68 TTCTAGCACCATCTGAAATCGGTTAT hsa-mir-029c-prec ACCACTGGCCCATCTCTTACACAGGCTGACCGATTTCT 69 CCTGGTGTTCAGAGTCTGTTTTTGTCTAGCACCATTTG AAATCGGTTATGATGTAGGGGGAAAAGCAGCAGC hsa-mir-030a-prec GCGACTGTAAACATCCTCGACTGGAAGCTGTGAAGCC 70 ACAGATGGGCTTTCAGTCGGATGTTTGCAGCTGC hsa-mir-030b- ATGTAAACATCCTACACTCAGCTGTAATACATGGATT 71 prec GGCTGGGAGGTGGATGTTTACGT hsa-mir-030b- ACCAAGTTTCAGTTCATGTAAACATCCTACACTCAGCT 72 prec GTAATACATGGATTGGCTGGGAGGTGGATGTTTACTT CAGCTGACTTGGA hsa-mir-030c-prec AGATACTGTAAACATCCTACACTCTCAGCTGTGGAAA 73 GTAAGAAAGCTGGGAGAAGGCTGTTTACTCTTTCT hsa-mir-030d- GTTGTTGTAAACATCCCCGACTGGAAGCTGTAAGACA 74 prec CAGCTAAGCTTTCAGTCAGATGTTTGCTGCTAC hsa-mir-031-prec GGAGAGGAGGCAAGATGCTGGCATAGCTGTTGAACTG 75 GGAACCTGCTATGCCAACATATTGCCATCTTTCC hsa-mir-032-prec GGAGATATTGCACATTACTAAGTTGCATGTTGTCACG 76 GCCTCAATGCAATTTAGTGTGTGTGATATTTTC hsa-mir-033b- GGGGGCCGAGAGAGGCGGGCGGCCCCGCGGTGCATT 77 prec GCTGTTGCATTGCACGTGTGTGAGGCGGGTGCAGTGC CTCGGCAGTGCAGCCCGGAGCCGGCCCCTGGCACCAC hsa-mir-033-prec CTGTGGTGCATTGTAGTTGCATTGCATGTTCTGGTGGT 78 ACCCATGCAATGTTTCCACAGTGCATCACAG hsa-mir-034-prec GGCCAGCTGTGAGTGTTTCTTTGGCAGTGTCTTAGCTG 79 GTTG TTGTGAGCAATAGTAAGGAAGCAATCAGCAAGT ATACTGCCCTAGAAGTGCTGCACGTTGTGGGGCCC hsa-mir-091-prec- TCAGAATAATGTCAAAGTGCTTACAGTGCAGGTAGTG 80 13 ATATGTGCATCTACTGCAGTGAAGGCACTTGTAGCATT ATGGTGA hsa-mir-092-prec- CTTTCTACACAGGTTGGGATCGGTTGCAATGCTGTGTT 81 13 = 092-1 TCTGTATGGTATTGCACTTGTCCCGGCCTGTTGAGTTT GG hsa-mir-092-prec- TCATCCCTGGGTGGGGATTTGTTGCATTACTTGTGTTC 82 X = 092-2 TATATAAAGTATTGCACTTGTCCCGGCCTGTGGAAGA hsa-mir-093-prec- CTGGGGGCTCCAAAGTGCTGTTCGTGCAGGTAGTGTG 83 7.1 = 093-1 ATTACCCAACCTACTGCTGAGCTAGCACTTCCCGAGCC CCCGG hsa-mir-093-prec- CTGGGGGCTCCAAAGTGCTGTTCGTGCAGGTAGTGTG 84 7.2 = 093-2 ATTACCCAACCTACTGCTGAGCTAGCACTTCCCGAGCC CCCGG hsa-mir-095-prec- AACACAGTGGGCACTCAATAAATGTCTGTTGAATTGA 85 4 AATGCGTTACATTCAACGGGTATTTATTGAGCACCCAC TCTGTG hsa-mir-096-prec- TGGCCGATTTTGGCACTAGCACATTTTTGCTTGTGTCT 86 7 CTCCGCTCTGAGCAATCATGTGCAGTGCCAATATGGG AAA hsa-mir-098-prec- GTGAGGTAGTAAGTTGTATTGTTGTGGGGTAGGGATA 87 X TTAGGCCCCAATTAGAAGATAACTATACAACTTACTA CTTTCC hsa-mir-099b- GGCACCCACCCGTAGAACCGACCTTGCGGGGCCTTCG 88 prec-19 CCGCACACAAGCTCGTGTCTGTGGGTCCGTGTC hsa-mir-099-prec- CCCATTGGCATAAACCCGTAGATCCGATCTTGTGGTG 89 21 AAGTGGACCGCACAAGCTCGCTTCTATGGGTCTGTGT CAGTGTG hsa-mir-100-1/2- AAGAGAGAAGATATTGAGGCCTGTTGCCACAAACCCG 90 prec TAGATCCGAACTTGTGGTATTAGTCCGCACAAGCTTGT ATCTATAGGTATGTGTCTGTTAGGCAATCTCAC hsa-mir-100-prec- CCTGTTGCCACAAACCCGTAGATCCGAACTTGTGGTAT 91 11 TAGTCCGCACAAGCTTGTATCTATAGGTATGTGTCTGT TAGG hsa-mir-101-1/2- AGGCTGCCCTGGCTCAGTTATCACAGTGCTGATGCTGT 92 prec CTATTCTAAAGGTACAGTACTGTGATAACTGAAGGAT GGCAGCCATCTTACCTTCCATCAGAGGAGCCTCAC hsa-mir-101-prec TCAGTTATCACAGTGCTGATGCTGTCCATTCTAAAGGT 93 ACAGTACTGTGATAACTGA hsa-mir-101-prec- TGCCCTGGCTCAGTTATCACAGTGCTGATGCTGTCTAT 94 1 TCTAAAGGTACAGTACTGTGATAACTGAAGGATGGCA hsa-mir-101-prec- TGTCCTTTTTCGGTTATCATGGTACCGATGCTGTATAT 95 9 CTGAAAGGTACAGTACTGTGATAACTGAAGAATGGTG hsa-mir-102-prec- CTTCTGGAAGCTGGTTTCACATGGTGGCTTAGATTTTT 96 1 CCATCTTTGTATCTAGCACCATTTGAAATCAGTGTTTT AGGAG hsa-mir-102-prec- CTTCAGGAAGCTGGTTTCATATGGTGGTTTAGATTTAA 97 7.1 ATAGTGATTGTCTAGCACCATTTGAAATCAGTGTTCTT GGGGG hsa-mir-102-prec- CTTCAGGAAGCTGGTTTCATATGGTGGTTTAGATTTAA 98 7.2 ATAGTGATTGTCTAGCACCATTTGAAATCAGTGTTCTT GGGGG hsa-mir-103-2- TTGTGCTTTCAGCTTCTTTACAGTGCTGCCTTGTAGCA 99 prec TTCAGGTCAAGCAACATTGTACAGGGCTATGAAAGAA CCA hsa-mir-103-prec- TTGTGCTTTCAGCTTCTTTACAGTGCTGCCTTGTAGCA 100 20 TTCAGGTCAAGCAACATTGTACAGGGCTATGAAAGAA CCA hsa-mir-103-prec- TACTGCCCTCGGCTTCTTTACAGTGCTGCCTTGTTGCA 101 5 = 103-1 TATGGATCAAGCAGCATTGTACAGGGCTATGAAGGCA TTG hsa-mir-104-prec- AAATGTCAGACAGCCCATCGACTGGTGTTGCCATGAG 102 17 ATTCAACAGTCAACATCAGTCTGATAAGCTACCCGAC AAGG hsa-mir-105-prec- TGTGCATCGTGGTCAAATGCTCAGACTCCTGTGGTGGC 103 X.1 = 105-1 TGCTCATGCACCACGGATGTTTGAGCATGTGCTACGGT GTCTA hsa-mir-105-prec- TGTGCATCGTGGTCAAATGCTCAGACTCCTGTGGTGGC 104 X.2 = 105-2 TGCTCATGCACCACGGATGTTTGAGCATGTGCTACGGT GTCTA hsa-mir-106-prec- CCTTGGCCATGTAAAAGTGCTTACAGTGCAGGTAGCT 105 X TTTTGAGATCTACTGCAATGTAAGCACTTCTTACATTA CCATGG hsa-mir-107-prec- CTCTCTGCTTTCAGCTTCTTTACAGTGTTGCCTTGTGGC 106 10 ATGGAGTTCAAGCAGCATTGTACAGGGCTATCAAAGC ACAGA hsa-mir-122a-prec CCTTAGCAGAGCTGTGGAGTGTGACAATGGTGTTTGT 107 GTCTAAACTATCAAACGCCATTATCACACTAAATAGC TACTGCTAGGC hsa-mir-122a-prec AGCTGTGGAGTGTGACAATGGTGTTTGTGTCCAAACT 108 ATCAAACGCCATTATCACACTAAATAGCT hsa-mir-123-prec ACATTATTACTTTTGGTACGCGCTGTGACACTTCAAAC 109 TCGTACCGTGAGTAATAATGCGC hsa-mir-124a-1- tccttcctCAGGAGAAAGGCCTCTCTCTCCGTGTTCACAGC 110 prec GGACCTTGATTTAAATGTCCATACAATTAAGGCACGC GGTGAATGCCAAGAATGGGGCT hsa-mir-124a-1- AGGCCTCTCTCTCCGTGTTCACAGCGGACCTTGATTTA 111 prec AATGTCCATACAATTAAGGCACGCGGTGAATGCCAAG AATGGGGCTG hsa-mir-124a-2- ATCAAGATTAGAGGCTCTGCTCTCCGTGTTCACAGCG 112 prec GACCTTGATTTAATGTCATACAATTAAGGCACGCGGT GAATGCCAAGAGCGGAGCCTACGGCTGCACTTGAAG hsa-mir-124a-3- CCCGCCCCAGCCCTGAGGGCCCCTCTGCGTGTTCACA 113 prec GCGGACCTTGATTTAATGTCTATACAATTAAGGCACG CGGTGAATGCCAAGAGAGGCGCCTCCGCCGCTCCTT hsa-mir-124a-3- TGAGGGCCCCTCTGCGTGTTCACAGCGGACCTTGATTT 114 prec AATGTCTATACAATTAAGGCACGCGGTGAATGCCAAG AGAGGCGCCTCC hsa-mir-124a-prec CTCTGCGTGTTCACAGCGGACCTTGATTTAATGTCTAT 115 ACAATTAAGGCACGCGGTGAATGCCAAGAG hsa-mir-124b- CTCTCCGTGTTCACAGCGGACCTTGATTTAATGTCATA 116 prec CAATTAAGGCACGCGGTGAATGCCAAGAG hsa-mir-125a-prec TGCCAGTCTCTAGGTCCCTGAGACCCTTTAACCTGTGA 117 GGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCT GGCGTCTGGCC hsa-mir-125a-prec GGTCCCTGAGACCCTTTAACCTGTGAGGACATCCAGG 118 GTCACAGGTGAGGTTCTTGGGAGCCTGG hsa-mir-125b-1 ACATTGTTGCGCTCCTCTCAGTCCCTGAGACCCTAACT 119 TGTGATGTTTACCGTTTAAATCCACGGGTTAGGCTCTT GGGAGCTGCGAGTCGTGCTTTTGCATCCTGGA hsa-mir-125b-1 TGCGCTCCTCTCAGTCCCTGAGACCCTAACTTGTGATG 120 TTTACCGTTTAAATCCACGGGTTAGGCTCTTGGGAGCT GCGAGTCGTGCT hsa-mir-125b-2- ACCAGACTTTTCCTAGTCCCTGAGACCCTAACTTGTGA 121 prec GGTATTTTAGTAACATCACAAGTCAGGCTCTTGGGAC CTAGGCGGAGGGGA hsa-mir-125b-2- CCTAGTCCCTGAGACCCTAACTTGTGAGGTATTTTAGT 122 prec AACATCACAAGTCAGGCTCTTGGGACCTAGGC hsa-mir-126-prec CGCTGGCGACGGGACATTATTACTTTTGGTACGCGCTG 123 TGACACTTCAAACTCGTACCGTGAGTAATAATGCGCC GTCCACGGCA hsa-mir-126-prec ACATTATTACTTTTGGTACGCGCTGTGACACTTCAAAC 124 TCGTACCGTGAGTAATAATGCGC hsa-mir-127-prec TGTGATCACTGTCTCCAGCCTGCTGAAGCTCAGAGGG 125 CTCTGATTCAGAAAGATCATCGGATCCGTCTGAGCTTG GCTGGTCGGAAGTCTCATCATC hsa-mir-127-prec CCAGCCTGCTGAAGCTCAGAGGGCTCTGATTCAGAAA 126 GATCATCGGATCCGTCTGAGCTTGGCTGGTCGG hsa-mir-128a-prec TGAGCTGTTGGATTCGGGGCCGTAGCACTGTCTGAGA 127 GGTTTACATTTCTCACAGTGAACCGGTCTCTTTTTCAG CTGCTTC hsa-mir-128b- GCCCGGCAGCCACTGTGCAGTGGGAAGGGGGGCCGAT 128 prec ACACTGTACGAGAGTGAGTAGCAGGTCTCACAGTGAA CCGGTCTCTTTCCCTACTGTGTCACACTCCTAATGG hsa-mir-128-prec GTTGGATTCGGGGCCGTAGCACTGTCTGAGAGGTTTA 129 CATTTCTCACAGTGAACCGGTCTCTTTTTCAGC hsa-mir-129-prec TGGATCTTTTTGCGGTCTGGGCTTGCTGTTCCTCTCAA 130 CAGTAGTCAGGAAGCCCTTACCCCAAAAAGTATCTA hsa-mir-130a-prec TGCTGCTGGCCAGAGCTCTTTTCACATTGTGCTACTGT 131 CTGCACCTGTCACTAGCAGTGCAATGTTAAAAGGGCA TTGGCCGTGTAGTG hsa-mir-131-1- gccaggaggcggGGTTGGTTGTTATCTTTGGTTATCTAGCTG 132 prec TATGAGTGGTGTGGAGTCTTCATAAAGCTAGATAACC GAAAGTAAAAATAACCCCATACACTGCGCAG hsa-mir-131-3- CACGGCGCGGCAGCGGCACTGGCTAAGGGAGGCCCGT 133 prec TTCTCTCTTTGGTTATCTAGCTGTATGAGTGCCACAGA GCCGTCATAAAGCTAgataaccgaaagtagaaatg hsa-mir-131-prec GTTGTTATCTTTGGTTATCTAGCTGTATGAGTGTATTG 134 GTCTTCATAAAGCTAGATAACCGAAAGTAAAAAC hsa-mir-132-prec CCGCCCCCGCGTCTCCAGGGCAACCGTGGCTTTCGATT 135 GTTACTGTGGGAACTGGAGGTAACAGTCTACAGCCAT GGTCGCCCCGCAGCACGCCCACGCGC hsa-mir-132-prec GGGCAACCGTGGCTTTCGATTGTTACTGTGGGAACTG 136 GAGGTAACAGTCTACAGCCATGGTCGCCC hsa-mir-133a-1 ACAATGCTTTGCTAGAGCTGGTAAAATGGAACCAAAT 137 CGCCTCTTCAATGGATTTGGTCCCCTTCAACCAGCTGT AGCTATGCATTGA hsa-mir-133a-2 GGGAGCCAAATGCTTTGCTAGAGCTGGTAAAATGGAA 138 CCAAATCGACTGTCCAATGGATTTGGTCCCCTTCAACC AGCTGTAGCTGTGCATTGATGGCGCCG hsa-mir-133-prec GCTAGAGCTGGTAAAATGGAACCAAATCGCCTCTTCA 139 ATGGATTTGGTCCCCTTCAACCAGCTGTAGC hsa-mir-134-prec CAGGGTGTGTGACTGGTTGACCAGAGGGGCATGCACT 140 GTGTTCACCCTGTGGGCCACCTAGTCACCAACCCTC hsa-mir-134-prec AGGGTGTGTGACTGGTTGACCAGAGGGGCATGCACTG 141 TGTTCACCCTGTGGGCCACCTAGTCACCAACCCT hsa-mir-135-1- AGGCCTCGCTGTTCTCTATGGCTTTTTATTCCTATGTG 142 prec ATTCTACTGCTCACTCATATAGGGATTGGAGCCGTGGC GCACGGCGGGGACA hsa-mir-135-2- AGATAAATTCACTCTAGTGCTTTATGGCTTTTTATTCC 143 prec TATGTGATAGTAATAAAGTCTCATGTAGGGATGGAAG CCATGAAATACATTGTGAAAAATCA hsa-mir-135-prec CTATGGCTTTTTATTCCTATGTGATTCTACTGCTCACTC 144 ATATAGGGATTGGAGCCGTGG hsa-mir-136-prec TGAGCCCTCGGAGGACTCCATTTGTTTTGATGATGGAT 145 TCTTATGCTCCATCATCGTCTCAAATGAGTCTTCAGAG GGTTCT hsa-mir-136-prec GAGGACTCCATTTGTTTTGATGATGGATTCTTATGCTC 146 CATCATCGTCTCAAATGAGTCTTC hsa-mir-137-prec CTTCGGTGACGGGTATTCTTGGGTGGATAATACGGATT 147 ACGTTGTTATTGCTTAAGAATACGCGTAGTCGAGG hsa-mir-138-1- CCCTGGCATGGTGTGGTGGGGCAGCTGGTGTTGTGAA 148 prec TCAGGCCGTTGCCAATCAGAGAACGGCTACTTCACAA CACCAGGGCCACACCACACTACAGG hsa-mir-138-2- CGTTGCTGCAGCTGGTGTTGTGAATCAGGCCGACGAG 149 prec CAGCGCATCCTCTTACCCGGCTATTTCACGACACCAGG GTTGCATCA hsa-mir-138-prec CAGCTGGTGTTGTGAATCAGGCCGACGAGCAGCGCAT 150 CCTCTTACCCGGCTATTTCACGACACCAGGGTTG hsa-mir-139-prec GTGTATTCTACAGTGCACGTGTCTCCAGTGTGGCTCGG 151 AGGCTGGAGACGCGGCCCTGTTGGAGTAAC hsa-mir-140 TGTGTCTCTCTCTGTGTCCTGCCAGTGGTTTTACCCTAT 152 GGTAGGTTACGTCATGCTGTTCTACCACAGGGTAGAA CCACGGACAGGATACCGGGGCACC hsa-mir-140as- TCCTGCCAGTGGTTTTACCCTATGGTAGGTTACGTCAT 153 prec GCTGTTCTACCACAGGGTAGAACCACGGACAGGA hsa-mir-140s-prec CCTGCCAGTGGTTTTACCCTATGGTAGGTTACGTCATG 154 CTGTTCTACCACAGGGTAGAACCACGGACAGG hsa-mir-141-prec CGGCCGGCCCTGGGTCCATCTTCCAGTACAGTGTTGG 155 ATGGTCTAATTGTGAAGCTCCTAACACTGTCTGGTAAA GATGGCTCCCGGGTGGGTTC hsa-mir-141-prec GGGTCCATCTTCCAGTACAGTGTTGGATGGTCTAATTG 156 TGAAGCTCCTAACACTGTCTGGTAAAGATGGCCC hsa-mir-142as- ACCCATAAAGTAGAAAGCACTACTAACAGCACTGGAG 157 prec GGTGTAGTGTTTCCTACTTTATGGATG hsa-mir-142-prec GACAGTGCAGTCACCCATAAAGTAGAAAGCACTACTA 158 ACAGCACTGGAGGGTGTAGTGTTTCCTACTTTATGGAT GAGTGTACTGTG hsa-mir-142s-pres ACCCATAAAGTAGAAAGCACTACTAACAGCACTGGAG 159 GGTGTAGTGTTTCCTACTTTATGGATG hsa-mir-143-prec GCGCAGCGCCCTGTCTCCCAGCCTGAGGTGCAGTGCT 160 GCATCTCTGGTCAGTTGGGAGTCTGAGATGAAGCACT GTAGCTCAGGAAGAGAGAAGTTGTTCTGCAGC hsa-mir-143-prec CCTGAGGTGCAGTGCTGCATCTCTGGTCAGTTGGGAG 161 TCTGAGATGAAGCACTGTAGCTCAGG hsa-mir-144-prec TGGGGCCCTGGCTGGGATATCATCATATACTGTAAGTT 162 TGCGATGAGACACTACAGTATAGATGATGTACTAGTC CGGGCACCCCC hsa-mir-144-prec GGCTGGGATATCATCATATACTGTAAGTTTGCGATGA 163 GACACTACAGTATAGATGATGTACTAGTC hsa-mir-145-prec CACCTTGTCCTCACGGTCCAGTTTTCCCAGGAATCCCT 164 TAGATGCTAAGATGGGGATTCCTGGAAATACTGTTCTT GAGGTCATGGTT hsa-mir-145-prec CTCACGGTCCAGTTTTCCCAGGAATCCCTTAGATGCTA 165 AGATGGGGATTCCTGGAAATACTGTTCTTGAG hsa-mir-146-prec CCGATGTGTATCCTCAGCTTTGAGAACTGAATTCCATG 166 GGTTGTGTCAGTGTCAGACCTCTGAAATTCAGTTCTTC AGCTGGGATATCTCTGTCATCGT hsa-mir-146-prec AGCTTTGAGAACTGAATTCCATGGGTTGTGTCAGTGTC 167 AGACCTGTGAAATTCAGTTCTTCAGCT hsa-mir-147-prec AATCTAAAGACAACATTTCTGCACACACACCAGACTA 168 TGGAAGCCAGTGTGTGGAAATGCTTCTGCTAGATT hsa-mir-148-prec GAGGCAAAGTTCTGAGACACTCCGACTCTGAGTATGA 169 TAGAAGTCAGTGCACTACAGAACTTTGTCTC hsa-mir-149-prec GCCGGCGCCCGAGCTCTGGCTCCGTGTCTTCACTCCCG 170 TGCTTGTCCGAGGAGGGAGGGAGGGACGGGGGCTGT GCTGGGGCAGCTGGA hsa-mir-149-prec GCTCTGGCTCCGTGTCTTCACTCCCGTGCTTGTCCGAG 171 GAGGGAGGGAGGGAC hsa-mir-150-prec CTCCCCATGGCCCTGTCTCCCAACCCTTGTACCAGTGC 172 TGGGCTCAGACCCTGGTACAGGCCTGGGGGACAGGGA CCTGGGGAC hsa-mir-150-prec CCCTGTCTCCCAACCCTTGTACCAGTGCTGGGCTCAGA 173 CCCTGGTACAGGCCTGGGGGACAGGG hsa-mir-151-prec CCTGCCCTCGAGGAGCTCACAGTCTAGTATGTCTCATC 174 CCCTACTAGACTGAAGCTCCTTGAGGACAGG hsa-mir-152-prec TGTCCCCCCCGGCCCAGGTTCTGTGATACACTCCGACT 175 CGGGCTCTGGAGCAGTCAGTGCATGACAGAACTTGGG CCCGGAAGGACC hsa-mir-152-prec GGCCCAGGTTCTGTGATACACTCCGACTCGGGCTCTG 176 GAGCAGTCAGTGCATGACAGAACTTGGGCCCCGG hsa-mir-153-1- CTCACAGCTGCCAGTGTCATTTTTGTGATCTGCAGCTA 177 prec GTATTCTCACTCCAGTTGCATAGTCACAAAAGTGATCA TTGGCAGGTGTGGC hsa-mir-153-1- tctctctctccctcACAGCTGCCAGTGTCA 178 prec TTGTCACAAAAGTGA TCATTGGCAGGTGTGGCTGCTGCATG hsa-mir-153-2- AGCGGTGGCCAGTGTCATTTTTGTGATGTTGCAGCTAG 179 prec TAATATGAGCCCAGTTGCATAGTCACAAAAGTGATCA TTGGAAACTGTG hsa-mir-153-2- CAGTGTCATTTTTGTGATGTTGCAGCTAGTAATATGAG 180 prec CCCAGTTGCATAGTCACAAAAGTGATCATTG hsa-mir-154-prec GTGGTACTTGAAGATAGGTTATCCGTGTTGCCTTCGCT 181 TTATTTGTGACGAATCATACACGGTTGACCTATTTTTC AGTACCAA hsa-mir-154-prec GAAGATAGGTTATCCGTGTTGCCTTCGCTTTATTTGTG 182 ACGAATCATACACGGTTGACCTATTTTT hsa-mir-155-prec CTGTTAATGCTAATCGTGATAGGGGTTTTTGCCTCCAA 183 CTGACTCCTACATATTAGCATTAACAG hsa-mir-16-2-prec CAATGTCAGCAGTGCCTTAGCAGCACGTAAATATTGG 184 CGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGC TGCTGAAGTAAGGTTGACCATACTCTACAGTTG hsa-mir-181a-prec AGAAGGGCTATCAGGCCAGCCTTCAGAGGACTCCAAG 185 GAACATTCAACGCTGTCGGTGAGTTTGGGATTTGAAA AAACCACTGACCGTTGACTGTACCTTGGGGTCCTTA hsa-mir-181b- TGAGTTTTGAGGTTGCTTCAGTGAACATTCAACGCTGT 186 prec CGGTGAGTTTGGAATTAAAATCAAAACCATCGACCGT TGATTGTACCCTATGGCTAACCATCATCTACTCCA hsa-mir-181c-prec CGGAAAATTTGCCAAGGGTTTGGGGGAACATTCAACC 187 TGTCGGTGAGTTTGGGCAGCTCAGGCAAACCATCGAC CGTTGAGTGGACCCTGAGGCCTGGAATTGCCATCCT hsa-mir-182-as- GAGCTGCTTGCCTCCCCCCGTTTTTGGCAATGGTAGAA 188 prec CTCACACTGGTGAGGTAACAGGATCCGGTGGTTCTAG ACTTGCCAACTATGGGGCGAGGACTCAGCCGGCAC hsa-mir-182-prec TTTTTGGCAATGGTAGAACTCACACTGGTGAGGTAAC 189 AGGATCCGGTGGTTCTAGACTTGCCAACTATGG hsa-mir-183-prec CCGCAGAGTGTGACTCCTGTTCTGTGTATGGCACTGGT 190 AGAATTCACTGTGAACAGTCTCAGTCAGTGAATTACC GAAGGGCCATAAACAGAGCAGAGACAGATCCACGA hsa-mir-184-prec CCAGTCACGTCCCCTTATCACTTTTCCAGCCCAGCTTT 191 GTGACTGTAAGTGTTGGACGGAGAACTGATAAGGGTA GGTGATTGA hsa-mir-184-prec CCTTATCACTTTTCCAGCCCAGCTTTGTGACTGTAAGT 192 GTTGGACGGAGAACTGATAAGGGTAGG hsa-mir-185-prec AGGGGGCGAGGGATTGGAGAGAAAGGCAGTTCCTGA 193 TGGTCCCCTCCCCAGGGGCTGGCTTTCCTCTGGTCCTT CCCTCCCA hsa-mir-185-prec AGGGATTGGAGAGAAAGGCAGTTCCTGATGGTCCCCT 194 CCCCAGGGGCTGGCTTTCCTCTGGTCCTT hsa-mir-186-prec TGCTTGTAACTTTCCAAAGAATTCTCCTTTTGGGCTTT 195 CTGGTTTTATTTTAAGCCCAAAGGTGAATTTTTTGGGA AGTTTGAGCT hsa-mir-186-prec ACTTTCCAAAGAATTCTCCTTTTGGGCTTTCTGGTTTTA 196 TTTTAAGCCCAAAGGTGAATTTTTTGGGAAGT hsa-mir-187-prec GGTCGGGCTCACCATGACACAGTGTGAGACTCGGGCT 197 ACAACACAGGACCCGGGGCGCTGCTCTGACCCCTCGT GTCTTGTGTTGCAGCCGGAGGGACGCAGGTCCGCA hsa-mir-188-prec TGCTCCCTCTCTCACATCCCTTGCATGGTGGAGGGTGA 198 GCTTTCTGAAAACCCCTCCCACATGCAGGGTTTGCAG GATGGCGAGCC hsa-mir-188-prec TCTCACATCCCTTGCATGGTGGAGGGTGAGCTTTCTGA 199 AAACCCCTCCCACATGCAGGGTTTGCAGGA hsa-mir-189-prec CTGTCGATTGGACCCGCCCTCCGGTGCCTACTGAGCTG 200 ATATCAGTTCTCATTTTACACACTGGCTCAGTTCAGCA GGAACAGGAGTCGAGCCCTTGAGCAA hsa-mir-189-prec CTCCGGTGCCTACTGAGCTGATATCAGTTCTCATTTTA 201 CACACTGGCTCAGTTCAGCAGGAACAGGAG hsa-mir-190-prec TGCAGGCCTCTGTGTGATATGTTTGATATATTAGGTTG 202 TTATTTAATCCAACTATATATCAAACATATTCCTACAG TGTCTTGCC hsa-mir-190-prec CTGTGTGATATGTTTGATATATTAGGTTGTTATTTAAT 203 CCAACTATATATCAAACATATTCCTACAG hsa-mir-191-prec CGGCTGGACAGCGGGCAACGGAATCCCAAAAGCAGC 204 TGTTGTCTCCAGAGCATTCCAGCTGCGCTTGGATTTCG TCCCCTGCTCTCCTGCCT hsa-mir-191-prec AGCGGGCAACGGAATCCCAAAAGCAGCTGTTGTCTCC 205 AGAGCATTCCAGCTGCGCTTGGATTTCGTCCCCTGCT hsa-mir-192-2/3 CCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTG 206 ACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTC CATAGGTCACAGGTATGTTCGCCTCAATGCCAG hsa-mir-192-prec GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATT 207 GACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATT CCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC hsa-mir-193-prec CGAGGATGGGAGCTGAGGGCTGGGTCTTTGCGGGCGA 208 GATGAGGGTGTCGGATCAACTGGCCTACAAAGTCCCA GTTCTCGGCCCCCG hsa-mir-193-prec GCTGGGTCTTTGCGGGCGAGATGAGGGTGTCGGATCA 209 ACTGGCCTACAAAGTCCCAGT hsa-mir-194-prec ATGGTGTTATCAAGTGTAACAGCAACTCCATGTGGAC 210 TGTGTACCAATTTCCAGTGGAGATGCTGTTACTTTTGA TGGTTACCAA hsa-mir-194-prec GTGTAACAGCAACTCCATGTGGACTGTGTACCAATTTC 211 CAGTGGAGATGCTGTTACTTTTGAT hsa-mir-195-prec AGCTTCCCTGGCTCTAGCAGCACAGAAATATTGGCAC 212 AGGGAAGCGAGTCTGCCAATATTGGCTGTGCTGCTCC AGGCAGGGTGGTG hsa-mir-195-prec TAGCAGCACAGAAATATTGGCACAGGGAAGCG 213 AGTCTGCCAATATTGGCTGTGCTGCT hsa-mir-196-1- CTAGAGCTTGAATTGGAACTGCTGAGTGAATTAGGTA 214 prec GTTTCATGTTGTTGGGCCTGGGTTTCTGAACACAACAA CATTAAACCACCCGATTCACGGCAGTTACTGCTCC hsa-mir-196-1- GTGAATTAGGTAGTTTCATGTTGTTGGGCCTGGGTTTC 215 prec TGAACACAACAACATTAAACCACCCGATTCAC hsa-mir-196-2- TGCTCGCTCAGCTGATCTGTGGCTTAGGTAGTTTCATG 216 prec TTGTTGGGATTGAGTTTTGAACTCGGCAACAAGAAAC TGCCTGAGTTACATCAGTCGGTTTTCGTCGAGGGC hsa-mir-196-prec GTGAATTAGGTAGTTTCATGTTGTTGGGCCTGGGTTTC 217 TGAACACAACAACATTAAACCACCCGATTCAC hsa-mir-197-prec GGCTGTGCCGGGTAGAGAGGGCAGTGGGAGGTAAGA 218 GCTCTTCACCCTTCACCACCTTCTCCACCCAGCATGGC C hsa-mir-198-prec TCATTGGTCCAGAGGGGAGATAGGTTCCTGTGATTTTT 219 CCTTCTTCTCTATAGAATAAATGA hsa-mir-199a-1- GCCAACCCAGTGTTCAGACTACCTGTTCAGGAGGCTC 220 prec TCAATGTGTACAGTAGTCTGCACATTGGTTAGGC hsa-mir-199a-2- AGGAAGCTTCTGGAGATCCTGCTCCGTCGCCCCAGTG 221 prec TTCAGACTACCTGTTCAGGACAATGCCGTTGTACAGTA GTCTGCACATTGGTTAGACTGGGCAAGGGAGAGCA hsa-mir-199b- CCAGAGGACACCTCCACTCCGTCTACCCAGTGTTTAG 222 prec ACTATCTGTTCAGGACTCCCAAATTGTACAGTAGTCTG CACATTGGTTAGGCTGGGCTGGGTTAGACCCTCGG hsa-mir-199s-prec GCCAACCCAGTGTTCAGACTACCTGTTCAGGAGGCTC 223 TCAATGTGTACAGTAGTCTGCACATTGGTTAGGC hsa-mir-200a-prec GCCGTGGCCATCTTACTGGGCAGCATTGGATGGAGTC 224 AGGTCTCTAATACTGCCTGGTAATGATGACGGC hsa-mir-200b- CCAGCTCGGGCAGCCGTGGCCATCTTACTGGGCAGCA 225 prec TTGGATGGAGTCAGGTCTCTAATACTGCCTGGTAATG ATGACGGCGGAGCCCTGCACG hsa-mir-202-prec GTTCCTTTTTCCTATGCATATACTTCTTTGAGGATCTGG 226 CCTAAAGAGGTATAGGGCATGGGAAGATGGAGC hsa-mir-203-prec GTGTTGGGGACTCGCGCGCTGGGTCCAGTGGTTCTTA 227 ACAGTTCAACAGTTCTGTAGCGCAATTGTGAAATGTTT AGGACCACTAGACCCGGCGGGCGCGGCGACAGCGA hsa-mir-204-prec GGCTACAGTCTTTCTTCATGTGACTCGTGGACTTCCCT 228 TTGTCATCCTATGCCTGAGAATATATGAAGGAGGCTG GGAAGGCAAAGGGACGTTCAATTGTCATCACTGGC hsa-mir-205-prec AAAGATCCTCAGACAATCCATGTGCTTCTCTTGTCCTT 229 CATTCCACCGGAGTCTGTCTCATACCCAACCAGATTTC AGTGGAGTGAAGTTCAGGAGGCATGGAGCTGACA hsa-mir-206-prec TGCTTCCCGAGGCCACATGCTTCTTTATATCCCCATAT 230 GGATTACTTTGCTATGGAATGTAAGGAAGTGTGTGGT TTCGGCAAGTG hsa-mir-206-prec AGGCCACATGCTTCTTTATATCCCCATATGGATTACTT 231 TGCTATGGAATGTAAGGAAGTGTGTGGTTTT hsa-mir-208-prec TGACGGGCGAGCTTTTGGCCCGGGTTATACCTGATGCT 232 CACGTATAAGACGAGCAAAAAGCTTGTTGGTCA hsa-mir-210-prec ACCCGGCAGTGCCTCCAGGCGCAGGGCAGCCCCTGCC 233 CACCGCACACTGCGCTGCCCCAGACCCACTGTGCGTG TGACAGCGGCTGATCTGTGCCTGGGCAGCGCGACCC hsa-mir-211-prec TCACCTGGCCATGTGACTTGTGGGCTTCCCTTTGTCAT 234 CCTTCGCCTAGGGCTCTGAGCAGGGCAGGGACAGCAA AGGGGTGCTCAGTTGTCACTTCCCACAGCACGGAG hsa-mir-212-prec CGGGGCACCCCGCCCGGACAGCGCGCCGGCACCTTGG 235 CTCTAGACTGCTTACTGCCCGGGCCGCCCTCAGTAACA GTCTCCAGTCACGGCCACCGACGCCTGGCCCCGCC hsa-mir-213-prec CCTGTGCAGAGATTATTTTTTAAAAGGTCACAATCAAC 236 ATTCATTGCTGTCGGTGGGTTGAACTGTGTGGACAAG CTCACTGAACAATGAATGCAACTGTGGCCCCGCTT hsa-mir-213-prec- GAGTTTTGAGGTTGCTTCAGTGAACATTCAACGCTGTC 237 LIM GGTGAGTTTGGAATTAAAATCAAAACCATCGACCGTT GATTGTACCCTATGGCTAACCATCATCTACTCC hsa-mir-214-prec GGCCTGGCTGGACAGAGTTGTCATGTGTCTGCCTGTCT 238 ACACTTGCTGTGCAGAACATCCGCTCACCTGTACAGC AGGCACAGACAGGCAGTCACATGACAACCCAGCCT hsa-mir-215-prec ATCATTCAGAAATGGTATACAGGAAAATGACCTATGA 239 ATTGACAGACAATATAGCTGAGTTTGTCTGTCATTTCT TTAGGCCAATATTCTGTATGACTGTGCTACTTCAA hsa-mir-216-prec GATGGCTGTGAGTTGGCTTAATCTCAGCTGGCAACTGT 240 GAGATGTTCATACAATCCCTCACAGTGGTCTCTGGGAT TATGCTAAACAGAGCAATTTCCTAGCCCTCACGA hsa-mir-217-prec AGTATAATTATTACATAGTTTTTGATGTCGCAGATACT 241 GCATCAGGAACTGATTGGATAAGAATCAGTCACCATC AGTTCCTAATGCATTGCCTTCAGCATCTAAACAAG hsa-mir-218-1- GTGATAATGTAGCGAGATTTTCTGTTGTGCTTGATCTA 242 prec ACCATGTGGTTGCGAGGTATGAGTAAAACATGGTTCC GTCAAGCACCATGGAACGTCACGCAGCTTTCTACA hsa-mir-218-2- GACCAGTCGCTGCGGGGCTTTCCTTTGTGCTTGATCTA 243 prec ACCATGTGGTGGAACGATGGAAACGGAACATGGTTCT GTCAAGCACCGCGGAAAGCACCGTGCTCTCCTGCA hsa-mir-219-prec CCGCCCCGGGCCGCGGCTCCTGATTGTCCAAACGCAA 244 TTCTCGAGTCTATGGCTCCGGCCGAGAGTTGAGTCTGG ACGTCCCGAGCCGCCGCCCCCAAACCTCGAGCGGG hsa-mir-220-prec GACAGTGTGGCATTGTAGGGCTCCACACCGTATCTGA 245 CACTTTGGGCGAGGGCACCATGCTGAAGGTGTTCATG ATGCGGTCTGGGAACTCCTCACGGATCTTACTGATG hsa-mir-221-prec TGAACATCCAGGTCTGGGGCATGAACCTGGCATACAA 246 TGTAGATTTCTGTGTTCGTTAGGCAACAGCTACATTGT CTGCTGGGTTTCAGGCTACCTGGAAACATGTTCTC hsa-mir-222-prec GCTGCTGGAAGGTGTAGGTACCCTCAATGGCTCAGTA 247 GCCAGTGTAGATCCTGTCTTTCGTAATCAGCAGCTACA TCTGGCTACTGGGTCTCTGATGGCATCTTCTAGCT hsa-mir-223-prec CCTGGCCTCCTGCAGTGCCACGCTCCGTGTATTTGACA 248 AGCTGAGTTGGACACTCCATGTGGTAGAGTGTCAGTT TGTCAAATACCCCAAGTGCGGCACATGCTTACCAG hsa-mir-224-prec GGGCTTTCAAGTCACTAGTGGTTCCGTTTAGTAGATGA 249 TTGTGCATTGTTTCAAAATGGTGCCCTAGTGACTACAA AGCCC hsA-mir-29b- CTTCTGGAAGCTGGTTTCACATGGTGGCTTAGATTTTT 250 1 = 102-prec1 CCATCTTTGTATCTAGCACCATTTGAAATCAGTGTTTT AGGAG hsA-mir-29b- CTTCAGGAAGCTGGTTTCATATGGTGGTTTAGATTTAA 251 2 = 102prec7.1 = ATAGTGATTGTCTAGCACCATTTGAAATCAGTGTTCTT 7.2 GGGGG hsA-mir-29b- CTTCAGGAAGCTGGTTTCATATGGTGGTTTAGATTTAA 252 3 = 102prec7.1 = ATAGTGATTGTCTAGCACCATTTGAAATCAGTGTTCTT 7.2 GGGGG hsa-mir-30* = GTGAGCGACTGTAAACATCCTCGACTGGAAGCTGTGA 253 mir-097-prec-6 AGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCTG CCTACT mir-033b ACCAAGTTTCAGTTCATGTAAACATCCTACACTCAGCT 254 GTAATACATGGATTGGCTGGGAGGTGGATGTTTACTT CAGCTGACTTGGA mir-101- TGCCCTGGCTCAGTTATCACAGTGCTGATGCTGTCTAT 255 precursor-9 = TCTAAAGGTACAGTACTGTGATAACTGAAGGATGGCA mir-101-3 mir-108-1-small ACACTGCAAGAACAATAAGGATTTTTAGGGGCATTAT 256 GACTGAGTCAGAAAACACAGCTGCCCCTGAAAGTCCC TCATTTTTCTTGCTGT mir-108-2-small ACTGCAAGAGCAATAAGGATTTTTAGGGGCATTATGA 257 TAGTGGAATGGAAACACATCTGCCCCCAAAAGTCCCT CATTTT mir-123-prec = CGCTGGCGACGGGACATTATTACTTTTGGTACGCGCTG 258 mir-126-prec TGACACTTCAAAC TCGTACCGTGAGTAATAATGCGCCGTCCACGGCA mir-123-prec = ACATTATTACTTTTGGTACGCGCTGTGACACTTCAAAC 259 mir-126-prec TCGTACCGTGAGTAATAATGCGC mir-129-1-prec TGGATCTTTTTGCGGTCTGGGCTTGCTGTTCCTCTCAA 260 CAGTAGTCAGGAAGCCCTTACCCCAAAAAGTATCTA mir-129-small- TGCCCTTCGCGAATCTTTTTGCGGTCTGGGCTTGCTGT 261 2 = 129b? ACATAACTCAATAGCCGGAAGCCCTTACCCCAAAAAG CATTTGCGGAGGGCG mir-133b-small GCCCCCTGCTCTGGCTGGTCAAACGGAACCAAGTCCG 262 TCTTCCTGAGAGGTTTGGTCCCCTTCAACCAGCTACAG CAGGG mir-135-small- AGATAAATTCACTCTAGTGCTTTATGGCTTTTTATTCC 263 TATGTGATAGTAATAAAGTCTCATGTAGGGATGGAAG CCATGAAATACATTGTGAAAAATCA mir-148b-small AAGCACGATTAGCATTTGAGGTGAAGTTCTGTTATAC 264 ACTCAGGCTGTGGCTCTCTGAAAGTCAGTGCAT mir-151-prec CCTGTCCTCAAGGAGCTTCAGTCTAGTAGGGGATGAG 265 ACATACTAGACTGTGAGCTCCTCGAGGGCAGG mir-155- CTGTTAATGCTAATCGTGATAGGGGTTTTTGCCTCCAA 266 prec(BIC) CTGACTCCTACATATTAGCATTAACAG mir-156 = mir- CCTAACACTGTCTGGTAAAGATGGCTCCCGGGTGGGT 267 157 = overlap mir- TCTCTCGGCAGTAACCTTCAGGGAGCCCTGAAGACCA 141 TGGAGGAC mir-158-small = GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATT 268 mir-192 GACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATT CCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC mir-159-1-small TCCCGCCCCCTGTAACAGCAACTCCATGTGGAAGTGC 269 CCACTGGTTCCAGTGGGGCTGCTGTTATCTGGGGCGA GGGCCA mir-161-small AAAGCTGGGTTGAGAGGGCGAAAAAGGATGAGGTGA 270 CTGGTCTGGGCTACGCTATGCTGCGGCGCTCGGG mir-163-1b-small CATTGGCCTCCTAAGCCAGGGATTGTGGGTTCGAGTC 271 CCACCCGGGGTAAAGAAAGGCCGAATT mir-163-3-small CCTAAGCCAGGGATTGTGGGTTCGAGTCCCACCTGGG 272 GTAGAGGTGAAAGTTCCTTTTACGGAATTTTTT mir-175- GGGCTTTCAAGTCACTAGTGGTTCCGTTTAGTAGATGA 273 small = mir-224 TTGTGCATTGTTTCAAAATGGTGCCCTAGTGACTACAA AGCCC mir-177-small ACGCAAGTGTCCTAAGGTGAGCTCAGGGAGCACAGAA 274 ACCTCCAGTGGAACAGAAGGGCAAAAGCTCATT mir-180-small CATGTGTCACTTTCAGGTGGAGTTTCAAGAGTCCCTTC 275 CTGGTTCACCGTCTCCTTTGCTCTTCCACAAC mir-187-prec GGTCGGGCTCACCATGACACAGTGTGAGACTCGGGCT 276 ACAACACAGGACCCGGGGCGCTGCTCTGACCCCTCGT GTCTTGTGTTGCAGCCGGAGGGACGCAGGTCCGCA mir-188-prec TGCTCCCTCTCTCACATCCCTTGCATGGTGGAGGGTGA 277 GCTTTCTGAAAACCCCTCCCACATGCAGGGTTTGCAG GATGGCGAGCC mir-190-prec TGCAGGCCTCTGTGTGATATGTTTGATATATTAGGTTG 278 TTATTTAATCCAACTATATATCAAACATATTCCTACAG TGTCTTGCC mir-197-2 GTGCATGTGTATGTATGTGTGCATGTGCATGTGTATGT 279 GTATGAGTGCATGCGTGTGTGC mir-197-prec GGCTGTGCCGGGTAGAGAGGGCAGTGGGAGGTAAGA 280 GCTCTTCACCCTTCACCACCTTCTCCACCCAGCATGGC C mir-202-prec GTTCCTTTTTCCTATGCATATACTTCTTTGAGGATCTGG 281 CCTAAAGAGGTATAGGGCATGGGAAGATGGAGC mir-294-1 (chr16) CAATCTTCCTTTATCATGGTATTGATTTTTCAGTGCTTC 282 CCTTTTGTGTGAGAGAAGATA mir-hes1 ATGGAGCTGCTCACCCTGTGGGCCTCAAATGTGGAGG 283 AACTATTCTGATGTCCAAGTGGAAAGTGCTGCGACAT TTGAGCGTCACCGGTGACGCCCATATCA mir-hes2 GCATCCCCTCAGCCTGTGGCACTCAAACTGTGGGGGC 284 ACTTTCTGCTCTCTGGTGAAAGTGCCGCCATCTTTTGA GTGTTACCGCTTGAGAAGACTCAACC mir-hes3 CGAGGAGCTCATACTGGGATACTCAAAATGGGGGCGC 285 TTTCCTTTTTGTCTGTTACTGGGAAGTGCTTCGATTTTG GGGTGTCCCTGTTTGAGTAGGGCATC hsa-mir-29b-1 CTTCAGGAAGCTGGTTTCATATGGTGGTTTAGATTTAA 664 ATAGTGATTGTCTAGCACCATTTGAAATCAGTGTTCTT GGGGG *An underlined sequence within a precursor sequence represents a processed miR transcript. All sequences are human.

Genome Analysis

The BUILD 33 and BUILD 34 Version 1 of the Homo sapiens genome, available at the NCBI website (see above), was used for genome analysis. For each human miR present in the miR database, a BLAST search was performed using the default parameters against the human genome to find the precise location, followed by mapping using the maps available at the Human Genome Resources at the NCBI website. See also Altschul et al. (1990), J. Mol. Biol. 215:403-10 and Altschul et al. (1997), Nucleic Acids Res. 25:3389-3402, the entire disclosures of which are herein incorporated by reference, for a discussion of the BLAST search algorithm. Also, as a confirmation of the data, the human clone corresponding to each miR was identified and mapped to the human genome (see Table 2). Perl scripts for the automatic submission of BLAST jobs and for the retrieval of the search results were based on the LPW, HTML, and HTPP Perl modules and BioPerl modules.

Fragile Site Database

This database was constructed using the Virtual Gene Nomenclature Workshop, maintained by the HUGO Gene Nomenclature Committee at University College, London. For each FRA locus, the literature was screened for publications reporting the cloning of the locus. In ten cases, genomic positions for both centromeric and telomeric ends were found. The total genomic length of these FRA loci is 26.9 Mb. In twenty-nine cases, only one anchoring marker was identified. It was determined, based on the published data, that 3 Mb can be used as the median length for each FRA locus. Therefore, 3 Mb was used as a guideline or window length for considering whether miR were in close proximity to the FRA sites.

The human clones for seventeen HPV16 integration sites (IS) were also precisely mapped on the human genome. By analogy with the length of a FRA, in the case of HPV16 integration sites, “close” vicinity was defined to be a distance of less than 2 Mb.

PubMed Database

The PubMed database was screened on-line for publications describing cancer-related abnormalities such as minimal regions of loss-of-heterozygosity (minimal LOH) and minimal regions of amplification (minimal amplicons) using the words “LOH and genome-wide,” “amplification and genome-wide” and “amplicon and cancer.” The PubMed database is maintained by the NCBI and was accessed via its website. The data obtained from thirty-two papers were used to screen for putative CAGRs, based on markers with high frequency of LOH/amplification. As a second step, a literature search was performed to determine the presence or absence of the above three types of alterations and to determine the precise location of miRs with respect to CAGRs (see above). Search phrases included the combinations “minimal regions of LOH AND cancer”, and “minimal region amplification AND cancer.” A total of 296 publications were found and manually curated to find regions defined by both telomeric and centromeric markers. One hundred fifty-four minimally deleted regions (median length-4.14 Mb) and 37 minimally amplified regions (median length-2.45 Mb) were identified with precise genomic mapping for both telomeric and centromeric ends involving all human chromosomes except Y. To identify common breakpoint regions, PubMed was searched with the combination “translocation AND cloning AND breakpoint AND cancer.” The search yielded 308 papers, which were then manually curated. Among these papers, 45 translocations with at least one breakpoint precisely mapped were reported.

Statistical Analyses

The incidence of miR genes and their association with specific chromosomes and chromosome regions, such as FRAs and amplified or deleted regions in cancer, was analyzed with random effect Poisson regression models. Under these models, “events” are defined as the number of miR genes, and non-overlapping lengths of the region of interest defined exposure “time” (i.e., fragile site versus non-fragile site, etc.). The “length” of a region was exactly ±1 Mb, if known, or estimated as ±1 Mb if unknown. The random effect used was chromosomal location, in that data within a chromosome were assumed to be correlated. The fixed effect in each model consisted of an indicator variable(s) for the type of region. This model provided the incidence rate ratio (IRR), 2-sided 95% confidence interval of the IRR, and 2-sided p-values for testing the hypothesis that the IRR is 1.0. An IRR significantly greater than 1 indicates an increase in the number of miR genes within a region.

Each model was repeated considering the distribution of miR genes only in the transcriptionally active portion of the genome (about 43% of the genome using the published data), rather than the entire chromosome length, and similar results were obtained. Considering the distribution of miRs only in the transcriptionally active portion of the genome is more conservative, and takes into account the phenomenon of clustering that was observed for the miR genes' genomic location. All computations were completed using STATA v7.0.

Patient Samples and Cell Lines

Patient samples were obtained from twelve chronic lymphocytic leukemia (CLL) patients, and mononuclear cells were isolated through Ficoll-Hypaque gradient centrifugation (Amersham Pharmacia Biotech, Piscataway, N.J.), as previously described (Calin et al., Proc. Natl. Acad. Sci. USA 2002, 99:15524-15529). Samples were then processed for RNA and DNA extraction according to standard protocols as described in Sambrook J et al. (1989), Molecular cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), the entire disclosure of which is herein incorporated by reference.

Seven human lung cancer cell lines were obtained from the American Type Culture Collection (ATCC; Manassas, Va.) and maintained according to ATCC instructions. These cell lines were: Calu-3, H1299, H522, H460, H23, H1650 and H1573.

Northern Blotting

Total RNA isolation from patient samples and cell lines described above was performed using the Tri-Reagent protocol (Molecular Research Center, Inc). RNA samples (30 μg each) were run on 15% acryl amide denaturing (urea) Criterion recast gels (Bio-Red Laboratories, Hercules, Calif.) and then transferred onto Hyoid-N+membrane (Amersham Pharmacia Biotech), as previously described (Calin et al., Proc. Natl. Acad. Sci. USA 2002, 99:15524-15529). Hybridization with gamma-³²P ATP labeled probes was performed at 42° C. in 7% SDS, 0.2 M Na₂PO₄, pH 7.0 overnight. Membranes were washed at 42° C., twice in 2×SSPE, 0.1% SDS and twice with 0.5×SSPE, 0.1% SDS. Blots were stripped by boiling in 0.1% aqueous SDS/0.1×SSC for 10 minutes, and were reprobed several times. As a gel loading control, 5S rRNA was also loaded and was stained with ethidium bromide. Lung tissue RNA was utilized as the normal control; normal lung total RNA was purchased from Clontech (Palo Alto, Calif.).

Example 1 miR Genes are Non-Randomly Distributed in the Human Genome

One hundred eighty-six human genes representing known or predicted miR genes were mapped, based on mouse homology or computational methods, as described above in the General Methods. The results are presented in Table 2. The names were as in the miRNA Registry; for new miR genes, sequential names were assigned. miR 213 from Sanger database is different from miR 213 described in Lim et al. (2003, Science 299:1540). MiR genes in clusters are separated by a forward slash “/”. The approximate location in Mb of each clone is presented in the last column.

TABLE 2 miR Database: Chromosome Location and Clustering Chromosome Loc (Mb) Name location Genes in Cluster (built 33) let-7a-1 09q22.2 let-7a-1/let-7f-1/let-7d 90.2-.3  let-7a-2 11q24.1 miR-125b-1/let-7a-2/miR-100  121.9-122.15 let-7a-3 22q13.3 let-7a-3/let-7b 44.7-.8  let-7b 22q13.3 let-7a-3/let-7b 44.7-.8  let-7c 21q11.2 miR-99a/let-7c/miR-125b-2 16.7-.9  let-7d 09q22.2 let-7a-1/let-7f-1/let7d 90.2-.3  let-7e 19q13.4 miR-99b/let-7e/miR-125a 56.75-57   let-7f-1 09q22.2 let-7a-1/let-7f-1/let7d 90.2-.3  let-7f-2 Xp11.2 miR-98/let-7f-2 52.2-.3  let-7g 03p21.3 let-7g/miR-135-1 52.1-.3  let-7i 12q14.1 62.7-.9  miR- 20q13.3 miR-133a-2/miR-1b-2 61.75-.8   001b-2 miR-001d 18q11.1 miR-133a-1/miR-1d 19.25-.4   miR-007-1 09q21.33   80-80.1 miR-007-2 15q25 86.7-.8  miR-007-3 19p13.3 4.7-.75 miR-009- 01q22 153.1-.2   1 (= miR- 131-1) miR-009- 05q14 87.85-88   2 (= miR- 131-2) miR-009- 15q25.3 87.5 3 (= miR- 131-3) miR-010a 17q21.3 miR-196-1/miR-10a 46.95-47.05 miR-010b 02q31 176.85-177   miR-015a 13q14 miR-16a/miR-15a 49.5-.8  miR-015b 03q26.1 miR-15b/miR-16b 161.35-.5   miR-016a 13q14 miR-16a/miR-15a 49.5-.8  miR-016b 03q26.1 miR-15b/miR-16b 161.35-.5   miR-017 13q31 miR-17/miR-18/miR-19a/miR-20/miR- 90.82 (= miR- 19b-1/miR-92-1 91) miR-018 13q31 miR-17/miR-18/miR-19a/miR-20/miR- 90.82 19b-1/miR-92-1 miR-019a 13q31 miR-17/miR-18/miR-19a/miR-20/miR- 90.82 19b-1/miR-92-1 miR- 13q31 miR-17/miR-18/miR-19a/miR-20/miR- 90.82 019b-1 19b-1/miR-92-1 miR- Xq26.2 miR-92-2/miR-19b-2/miR-106a 131.2-.3   019b-2 miR-020 13q31 miR-17/miR-18/miR-19a/miR-20/miR- 90.82 19b-1/miR-92-1 miR-021 17q23.2 58.25-.35  (= miR104- as) miR-022 17p13.3 1.4-.6  miR-023a 19p13.2 miR-24-2/miR-27a/miR-23a/miR- 13.75-.95  181c miR-023b 09q22.1 miR-24-1/miR27b/miR-23b 90.8-91   miR-024- 09q22.1 miR-24-1/miR27b/miR-23b 90.8-91   1 (= miR- 189) miR-024-2 19p13.2 miR-24-2/miR-27a/miR-23a/miR- 13.75-.95  181c miR-025 07q22 miR-106b/miR-25/miR-93-1 99.25-.4   miR-026a 03p21 37.8-.9  miR-026b 02q35 219.1-.3   miR-027a 19p13.2 miR-24-2/miR-27a/miR-23a/miR- 13.75-.95  181c miR-027b 09q22.1 miR-24-1/miR27b/miR-23b 90.8-91   miR-028 03q28 189.65-.85   miR-029a 07q32 miR-29a/miR29b 129.9-130.1 miR-029b 07q32 miR-29a/miR29b 129.9-130.1 (= miR- 102-7.1) miR-029c 01q32.2-32.3 miR-29c/miR-102 204.6-.7   miR-030a- 06q12-13 72.05-.2   as miR-030a- 06q12-13 72.05-.2   s (= miR- 097) miR-030b 08q24.2 miR-30d/miR-30b 135.5 miR-030c 06q13 71.95-72.1  miR-030d 08q24.2 miR-30d/miR-30b 135.5 miR-031 09p21 21.3-.5  miR-032 09q31.2 105.1-.3   miR-033a 22q13.2 40.5-.8  miR-033b 17p11.2 17.6-.7  miR-034 01p36.22 8.8 (= miR- 170) miR-034a-1 11q23 miR-34a-2/miR 34a-1 111.3-.5   miR-034a-2 11q23 miR-34a-2/miR 34a-1 111.3-.5   miR-092-1 13q31 miR-17/miR-18/miR-19a/miR-20/miR- 90.82 19b-1/miR-92-1 miR-092-2 Xq26.2 miR-92-2/miR-19b-2/miR-106a 131.2-.3   miR-093-1 07q22 miR-106b/miR-25/miR-93-1 99.25-.4   miR-095 04p16  8-.2 miR-096 07q32 miR-182s/miR-182as/miR-96/miR- 128.9-129   183 miR-098 Xp11.2 miR-98/let-7f-2 52.2-.3  miR-099a 21q11.2 miR-99a/let-7c/miR-125b-2 16.7-.9  miR-099b 19q13.4 miR-99b/let-7e/miR-125a 56.75-57   miR-100 11q24.1 miR-125b-1/let-7a-2/miR-100  121.9-122.15 miR-101-1 01p31.3 64.85-95   miR-101-2 09p24 4.8-5   miR-102 01q32.2-32.3 miR-29c/miR-102 204.5-.7   miR-103-1 05q35.1 167.8-.95  miR-103-2 20p13 3.82-.90  miR-105-1 Xq28 149.3-.4   miR-106b 07q22 miR-106b/miR-25/miR-93-1 99.25-.4   (= miR- 94) miR-106a Xq26.2 miR-92-2/miR-19b-2/miR-106a 131.2-.3   miR-107 10q23.31 91.45-.6   miR-108-1 17q11.1 miR-108-1/miR-193 29.6-.8  miR-108-2 16q13.1 14.3-.5  miR-122a 18q21 55.85-56   miR-123 09q34  132.9-133.05 (= miR- 126) miR-124a-1 08p23 9.5-.65 miR-124a-2 08q12.2 64.9-65.1 miR-124a-3 20q13.33 62.4-.55  miR-125a 19q13.4 miR-99b/let-7e/miR-125a 56.75-57   miR-125b-1 11q24.1 miR-125b1/let-7a-2/miR-100 121.9-122.1 miR-125b-2 21q11.2 miR-99a/let-7c/miR-125b-2 16.7-.9  miR-127 14q32 miR-127/miR-136 99.2-.4  miR-128a 02q21 136.3-.5   miR-128b 03p22 35.45-.6   miR-129-1 07q32 127.25-.4   miR-129-2 11p11.2 43.65-.75  miR-130a 11q12 57.6-.7  miR-130b 22q11.1 20.2-.4  miR-132 17p13.3 miR-212/miR-132 1.85-2   miR-133a-1 18q11.1 miR-133a-1/miR-1d 19.25-.4   miR-133a-2 20q13.3 miR-133a-2/miR-1b-2 61.75-.8   miR-133b 06p12 miR-206/miR-133b 51.9-52   miR-134 14q32 miR-154/miR-134/miR-299 99.4-.6  miR-135-1 03p21.3 let-7g/miR-135-1 52.1-.3  miR-135-2 12q23 97.85-98   miR-136 14q32 miR-127/miR-136 99.2-.4  miR-137 01p21-22 97.75 miR-138-1 03p21 43.85-.95  miR-138-2 16q12-13 56.55-.7   miR-139 11q13 72.55-.7   miR-140as 16q22.1 69.6-.8  miR-140s 16q22.1 69.6-.8  miR-141 12p13 overlap miR-156 - cluster  6.9-7.05 (= overlap miR-156) miR-142- 17q23 56.75-.9   as miR-142-s 17q23 56.75-.9   miR-143 05q32-33 miR-145/miR-143 148.65-.8   miR-144 17q11.2 27.05 miR-145 05q32-33 miR-145/miR-143 148.65-.8   miR-146 05q34 159.8-.9   miR-147 09q33 116.35-.55   miR-148 07p15 25.6-.8  miR-148b 12q13 54.35-.45  miR-149 02q37.3 241.3-.4   miR-150 19q13 54.6-.8  miR-151 08q24.3 141.4-.5   miR-152 17q21 46.4-.5  miR-153-1 02q36 220.1-.2   miR-153-2 07q36 156.5-.7   miR-154 14q32 miR-154/miR-134/miR-299 99.4-.6  miR-155 21q21 25.85 (BIC) miR-156 12p13 overlap miR-141 - cluster  6.9-7.05 (= miR- 157) miR-159-1 11q13 miR-159-1/miR-192 64.9-65   miR-161 08p21 21.8-.9  miR-175 Xq28 148.8-.9   (= miR- 224) miR-177 08p21 21.25-.35  miR-180 22q11.21-12.2 26.45 miR-181a 09q33.1-34.13 120.85-.95   (= miR- 178-2) miR-181b 01q31.2-q32.1 miR-213 S/miR-181b 195.2-.35  (= miR- 178 = miR-213- LIM) miR-181c 19p13.3 miR-24-2/miR-27a/miR-23a/miR- 13.75-.95  181c miR-182- 07q32 miR-182s/miR-182as/miR-96/miR- 128.9-129   as 183 miR-182-s 07q32 miR-182s/miR-182as/miR-96/miR- 128.9-129   183 miR-183 07q32 miR-182s/miR-182as/miR-96/miR- 128.9-129   (= miR- 183 174) miR-184 15q24 76.9-77.1 miR-185 22q11.2 18.35-.45  miR-186 01p31 70.9-71   miR-187 18q12.1 33.25-.4   miR-188 Xp11.23-p11.2 48.35-.5   miR-190 15q21 60.6-.8  miR-191 03p21 48.85-.95  miR-192 11q13 miR-159-1/miR-192 64.9-65   (= miR- 158) miR-193 17q11.2 miR-108-1/miR-193 29.6-.8  miR-194 01q41 miR-215/miR-194 216.7-.8   (= miR- 159-2) miR-195 17p13 6.75-.85  miR-196-1 17q21 miR-196-1/miR-10a 46.9-47.1 miR-196-2 12q13   54-54.15 miR-197 01p13 109.2-.3   miR-198 03q13.3 121.3-.4   miR-199a- 19p13.2 10.75-.8   1 (= miR- 199s) miR-199a-2 01q23.3 miR-214/miR-199a-2 168.7-.8   miR-199as 19p13.2 10.75-.8   (= antisense miR-199a- 1) miR-199b 09q34 124.3-.5   (= miR- 164) miR-200 01p36.3 0.9-1   miR-202 10q26.3 135 miR-203 14q32.33 102.4-.6   miR-204 09q21.1 66.9-67   miR-205 01q32.2 206.2-.3   miR-206 06p12 miR-206/miR-133b 51.9-52   miR-208 14q11.2 21.8-22   miR-210 11p15 0.55-0.75 miR-211 15q11.2-q12 28.9-29.1 miR-212 17p13.3 miR-212/miR-132 1.9-2.1 miR-213- 01q31.3-q32.1 miR-213 S/miR-181b 195.2-.35  SANGER miR-214 01q23.3 miR-214/miR-199a-2 168.7-.8   miR-215 01q41 miR-215/miR-194 216.7-.8   miR-216 02p16 miR-217/miR-216 56.2-.4  miR-217 02p16 miR-217/miR-216 56.2-.4  miR-218-1 04p15.32 20.15-.35  miR-218-2 05q35.1  168-.15  miR-219 06p21.2-21.31 33.1-.25  miR-220 Xq25 120.6-.8   miR-221 Xp11.3 miR-222/miR-221 44.35-.45  miR-222 Xp11.3 miR-222/miR-221 44.35-.45  miR-223 Xq12-13.3 63.4-.5  miR-294-1 16q22 65.1-.3  miR-297-3 20q13.2 52.25-.35  miR-299 14q32 miR-154/miR-134/miR-299 99.4-.6  miR-301 17q23 57.5-.7  miR-302 04q25 113.9-114   miR-hes1 19q13.4 miR-hes1/miR-hes2/miR-hes3  58.9-59.05 miR-hes2 19q13.4 miR-hes1/miR-hes2/miR-hes3  58.9-59.05 miR-hes3 19q13.4 miR-hes1/miR-hes2/miR-hes3  58.9-59.05

The distribution of the 186 human miR genes was found to be non-random. Ninety miR genes were located in 36 clusters, usually with two or three genes per cluster (median=2.5). The largest cluster found comprises six genes (miR-17/miR-18/miR-19a/miR-20/miR-19b1/miR-92-1) and is located at 13q31 (Table 2). A significant association of the incidence of miR genes with specific chromosomes was found. Chromosome 4 was found to have a lower than expected rate of miR genes (IRR=0.27; p=0.035). Chromosomes 17 and 19 were found to have significantly more miR genes than expected, based on chromosome size (IRR=2.97, p=0.002 and IRR=3.39, p=0.001, respectively). Six of the 36 miR gene clusters (17%), which contain 16 of 90 clustered genes (18%), are located on these two small chromosomes, which account for only 5% of the entire genome.

Similar results were obtained using a model considering the distribution of miR genes only in the transcriptionally active portion of the genome (see Table 3).

Chromosome 1 is used as the baseline in the model with a rate of miR gene incidence of ˜0.057, which is approximately equal to the overall rate of miR gene incidence across the genome.

TABLE 3 Location of miRs by chromosome and results of mixed effects Poisson regression model. Chromosome Length # of miRs IRR p  1 279 16 — —  2 251 7 0.49 0.112  3 221 10 0.79 0.557  4 197 3 0.27 0.035  5 198 6 0.53 0.183  6 176 6 0.59 0.277  7 163 13 1.39 0.377  8 148 6 0.71 0.469  9 140 15 1.87 0.082 10 143 2 0.24 0.060 11 148 11 1.29 0.508 12 142 6 0.74 0.523 13 118 8 0 1.000 14 107 7 1.14 0.771 15 100 5 0.87 0.789 16 104 5 0.84 0.731 17 88 15 2.97 0.002 18 86 4 0.81 0.708 19 72 14 3.39 0.001 20 66 5 1.32 0.587 21 45 4 1.55 0.433 22 48 6 2.09 0.123 X 163 12 1.28 0.513 Y 51 0 0 1.000

Example 2 miR Genes are Located in or Near Fragile Sites

Thirty-five of 186 miRs (19%) were found in (13 miR genes), or within 3 Mb (22 miR genes) of cloned fragile sites (FRA). A set of 39 fragile sites with available cloning information was used in the analysis. Data were available for the exact dimension (mean 2.69 Mb) and position of ten of these cloned fragile sites (see General Methods above). The relative incidence of miR genes inside fragile sites occurred at a rate 9.12 times higher than in non-fragile sites (p<0.001, using mixed effect Poisson regression models; see Tables 3 and 4). The same very high statistical significance was also found when only the 13 miRs located exactly inside a FRA or exactly in the vicinity of the “anchoring” marker mapped for a FRA were considered (IRR=3.21, p<0.001). Among the four most active common fragile sites (FRA3B, FRA16D, FRA6E, and FRA7H), the data demonstrate seven miRs in (miR-29a and miR-29b) or close (miR-96, miR-182s, miR-182 as, miR-183, and miR-129-1) to FRA7H, the only fragile site where no candidate tumor suppressor (TS) gene has been found. The other three of the four most active sites contain known or candidate TS genes; i.e., FHIT, WWOX and PARK2, respectively (Ohta et al., 1996, Cell 84:587-597; Paige et al., 2001, Proc. Natl. Acad. Sci. USA 98:11417-11422; Cesari et al., 2003, Proc. Natl. Acad. Sci. USA 100:5956-5961).

Analysis of 113 fragile sites scattered in the human karyotype showed that 61 miR genes are located in the same cytogenetic positions with FRAs. Thirty-five miR genes were located inside twelve cloned FRAs. These data indicate that more miRs are located in or near FRAs, and that the results described herein represent an underestimation of miR gene/FRA association, likely because the mapping of these unstable regions is not complete.

TABLE 4 Mixed Effect Poisson Regression Results for the Association Between microRNAs and Several Types of Regions of Interest Incidence Rate 95% CI Region of interest Ratio (IRR) IRR p Cloned Fragile sites vs. non- 9.12  6.22, 13.38 <0.001 fragile sites HPV16 insertion vs. all other 3.22 1.55, 6.68 <0.002 Deleted region vs. all other 4.08 2.99, 5.56 <0.001 Amplified region vs. all other 3.97 2.31, 6.83 <0.001 HOX Clusters vs. all other 15.77  7.39, 33.62 <0.001 Homeobox genes vs. all other 2.95 1.63, 5.34 <0.001 Note: “all other” means all the genome except the regions of interest.

Example 3 miR Genes are Located in or Near Human Papilloma Virus (HPV) Integration Sites

Because common fragile sites are preferential targets for HPV 16 integration in cervical tumors, and infection with HPV16 or HPV18 is the major risk factor for developing cervical cancer, the association between miR gene locations and HPV16 integration sites in cervical tumors was analyzed. The data indicate that thirteen miR genes (7%) are located within 2.5 Mb of seven of seventeen (45%) cloned integration sites. The relative incidence of miRs at HPV16 integration sites occurred at a rate 3.22 times higher than in the rest of the genome (p<0.002) (Tables 4 and 5). In one cluster of integration sites at chromosome 17q23, where three HPV16 integration sites are spread over roughly 4 Mb of genomic sequence, four miR genes (miR-21, miR-301, miR-142s and miR-142 as) were found.

TABLE 5 Analyzed FRA Sites, Cancer Correlation and HPV Integration Sites Distance Location miR- HPV16 Symbol Chromosome Cancer correlation Type (Mb) Closest miR(s) FRA(Mb) integration* FRA1A 1p36 FRA1C 1p31 aphidicolin type, 67.87 miR-186; miR- 3; 3 common 101-1 FRA1F 1q21 bladder FRA1H 1q42.1 cervical 5-azacytidine, 216.5 miR-194; miR- exact YES common 215 FRA2G 2q31 RCC FRA2I 2q33 chronic myelogenous leukemia FRA3B 3p14.2 esophageal carcinoma, lung, stomach, kidney, cervical cancer FRA4B 4q12 FRA4C 4q31.1 FRA5C 5q31.1 FRA5E 5p14 FRA6E 6q26 ovarian FRA6F 6q21 leukemias and solid tumors FRA7E 7q21.2 or 21.11 FRA7F 7q22 aphidicolin type, 100.2-107   miR-106b; miR- less than 1 common 25; miR-93 FRA7G 7q31.2 ovarian FRA7H 7q32.3 esophageal aphidicolin type, 129.8-130.4 miR-29b; miR- exact; 1 common 29a; and 2.5 miR-96; miR- 182s; miR-182as; miR-183; miR- 129-1 FRA7I 7q35 breast FRA8B 8q22.1 FRA8E 8q24.1 FRA9D 9q22.1 bladder aphidicolin type, 89.5-92   let7a-1; let-7d; exact common let-7f-1 miR-23b; miR-24-1; miR- 27b FRA9E 9q32-33.1 ovarian, bladder, aphidicolin type, 101.3-111.9 miR-32 exact YES cervical common FRA10B 10q25.2 FRA10C 10q21 FRA10D 10q22.1 FRA11A 11q13.3 hematopoietic and solid folic acid type, 66.18-66.9  miR-159-1; miR- 1.2 tumors rare 192 FRA11B 11q23.3 folic acid type, 119.1-.2   miR-125b-1; let- 2 rare 7a-2; miR-100 FRA12A 12q13.1 folic acid type, 53.55 miR-196-2; miR- 1 rare 148b FRA13C 13q21.2 FRA15A 15q22 aphidicolin type, 60.93 miR-190 exact common FRA16D 16q23.2 gastric adenocarcinoma, adenocarcinomas of stomach, colon, lung and ovary FRA16E 16p12.1 FRA17B 17q23.1 aphidicolin type, 58.25-58.35 miR-21 exact YES common miR-301 0.5 miR-142s; miR- 1.5 142as FRA18A 18q12.2 esophageal carcinoma FRA22A 22q13 FRAXA Xq27.31 FRAXB Xp22.3 FRAXE Xq28 FRAXF Xq28 146.58 miR-105-1; miR- 2.2 175 Note: *other microRNAs located close to HPV16 integration sites were found in relation to FRA5C, FRA11C, FRA12B and FRA12E. Positions are indicated according to Build 33 of the Human Genome.

Example 4 miR Genes are Located in or Near Cancer Associated Genomic Regions

Because the miR-FRA-HPV16 association has significance for cancer pathogenesis, miR genes might be involved in malignancies through other mechanisms, such as deletion, amplification, or epigenetic modifications. Thus, a search was performed for reported genomic alterations in human cancers, located in regions containing miR genes. PubMed was searched for reports of CAGR such as minimal regions of loss-of-heterozygosity (LOH) suggestive of the presence of tumor-suppressor genes (TSs), minimal regions of amplification suggestive of the presence of oncogenes (OGs), and common breakpoint regions in or near possible OGs or TSs (see General Methods above). Overall, 98 of 187 (52.5%) miR genes were found to be located in CAGRs (see Tables 6 and 7). Eighty of the miR genes (43%) were found to be located exactly within minimal regions of LOH or minimal regions of amplification described in a variety of tumors, such as lung, breast, ovarian, colon, gastric and hepatocellular carcinoma, as well as leukemias and lymphomas (see Tables 6 and 7).

The analysis showed that on chromosome 9, eight of fifteen mapped miR genes (including six located in clusters), were located inside two regions of deletion on 9q (Simoneau et al., 1999, Oncogene 7:157-163): the clusters let-7a-1/let-7f-1/let-7d and miR-23b/miR-27b/miR-24-1 inside region B at 9q22.3 and miR-181a and miR-199b inside region D at 9q33-34.1 (Table 6). Furthermore, five other miR genes were located less than 2 Mb from the markers with the highest rate of LOH: miR-31 near IFNA, miR-204 near D9S15, miR-181 and miR-147 near GSN, and miR-123 near D9S67.

In breast carcinomas, two different regions of loss at 11q23, independent from the ATM locus, have been studied extensively: the first spans about 2 Mb between loci D11S1347 and D11S927; the second is located between loci D11S1345 and D11S1316 and is estimated at about 1 Mb (di Iasio et al., 1999, Oncogene 25:1635-1638). Despite extensive effort, the only candidate TS gene found was the PPP2R1B gene, involved in less than 10% of reported cases (Calin et al., 2002, Proc. Natl. Acad. Sci. USA 99:15524-15529; Wang et al., 1998, Science 282:284-7). Both of these minimal LOH regions contained numerous microRNAs: the cluster miR-34-a1/miR-34-a2 in the first and the cluster miR-125b1/let-7a-2/miR-100 in the second.

High frequency LOH at 17p13.3 and relatively low TP53 mutation frequency in cases of hepatocellular carcinomas (HCC), lung cancers and astrocytomas indicate the presence of other TSs involved in the development of these tumors. One minimal LOH region correlated with HCC, and located telomeric to TP53 between markers D17S1866 and D17S1574 on chromosome 17, contained three miR genes: miR-22, miR-132, and miR-212. miR-195 is located between ENO3 and TP53 on chromosome 17.

Homozygous deletions (HD) in cancer can indicate the presence of TSs (Huebner et al., 1998, Annu Rev. Genet. 32:7-31), and several miR genes are located in homozygously deleted regions without known TSs. In addition to miR-15a and miR-16a located at 13q14 HD region in B-CLL, the cluster miR-99a/let-7c/miR-125b-2 mapped in a 21p11.1 region of HD in lung cancers and miR-32 at 9q31.2 in a region of HD in various types of cancer. Among the seven regions of LOH and HD on the short arm of chromosome 3, three of the regions harbor miRs: miR-26a in region AP20, miR-138-1 in region 5 at 3p21.3 and the cluster let-7g/miR-135-1 in region 3 at 3p21.1-p21.2. The locations of the miR genes/gene clusters are not likely to be random, because it was found that overall, the relative incidence of miRs in both deleted and amplified regions is highly significant (IRR=4.08, p<0.001 and IRR=3.97, p=0.001, respectively) (Table 4). Thus, these miRs expand the spectrum of candidate TSs.

TABLE 6 Examples of microRNAs Located in Minimal Deleted Regions, Minimal Amplified Regions, and Breakpoint Regions Involved in Human Cancers* Location (defining Size Known Chromosome markers) Mb MiR Gene Histotype OG/TS 3p21.1-21.2-D ARP- 7 let-7g/miR-135-1 lung, breast — DRR1 cancer 3p21.3(AP20)-D GOLGA4- 0.75 miR-26a epithelial cancer — VILL 3p23-21.31 D3S1768- 12.32 miR-26a; miR-138-1 nasopharyngeal — (MDR2)-D D3S1767 cancer 5q32-D ADRB2- 2.92 miR-145/miR-143 myelodysplastic — ATX1 syndrome 9q22.3-D D9S280- 1.46 miR-24-1/mir-27b/miR- urothelial cancer PTC, D9S1809 23b; FANCC let-7a-1/let-7f-1/let-7d 9q33-D D9S1826- 0.4 miR-123 NSCLC — D9S158 11q23-q24-D D11S927- 1.994 miR-34a-1/miR-34a-2 breast, lung PPP2R1B D11S1347 cancer 11q23-q24-D D11S1345- 1.725 miR-125b-1/let-7a- breast, lung, — D11S1328 2/miR-100 ovary, cervix cancer 13q14.3-D D13S272- 0.54 miR-15a/miR-16a B-CLL — D13S25 13q32-33-A stSG15303- 7.15 miR-17/miR-18/miR- follicular — stSG31624 19a/miR-20/miR-19b- lymphoma 1/miR-92-1 17p13.3-D D17S1866- 1.899 miR-22; miR-132; miR- HCC — D17S1574 212 17p13.3-D ENO3- 2.275 miR-195 lung cancer TP53 TP53 17q22-t(8; 17) miR-142s/ miR-142s; miR-142as prolymphocytic c-MYC c-MYC leukemia 17q23-A CLTC- 0.97 miR-21 neuroblastoma — PPM1D 20q13-A FLJ33887- 0.55 miR-297-3 colon cancer — ZNF217 21q11.1-D D21S1911- 2.84 miR-99a/let-7c/miR- lung cancer — ANA 125b Note: *OG—oncogene; TS—tumor suppressor gene; D—deleted region; A—amplified region; NSCLC—Non-Small Cell Lung Cancer; HCC—Hepatocellular carcinoma; B-CLL—B-Chronic Lymphocytic Leukemia; PTC—patched homolog (Drosophila); FANCC—Fanconi anemia, complementation group C; PPP2R1B—protein phosphatase 2, regulatory subunit A (PR 65), β isoform. miR genes in a cluster are separated by a slash.

TABLE 7 MicroRNAs Located in Minimal Deleted Regions, Minimal Amplified Regions and Breakpoint Regions Involved in Human Cancers Size/ miR Type of region Position Position Distance Location Chromosome (name) Marker 1 (Mb) Marker 2 (Mb) (Mb) Histotype Closest miR (Mb) 01p31 D D1S2638 62.92 ARHI 67.885 4.96 ovarian and miR-101-1 64.9 breast cancer 01p36.3 D D1S468 3.36 D1s2697 15.23 0 Non Small Cell miR-34 8.8 Lung Ca. 02q21 D D2S1334 136.66 0.1 gastric ca. miR-128a 136.55 02q37 D D2S125 241.5 0.2 hepatocellular miR-149 241.65 carcinoma (HCC) 03p21.1-21.2 D ARP 51.5 DRR1 58.5 7 lung, breast ca. let-7g/miR-135-1 52.3 03p21.3 D (AP20) GOLGA4 37.25 VILL 38 0.75 epithelial miR-26a 38 malignancies 03p23-21.31 D (MDR2) D3S1768 34.59 D3S1767 46.91 12.32 nasopharyngeal miR-26a; miR- 38; 44 carcinoma 138-1 03q27 t(3; 11)(q27; q23.1) LAZ3/BCL6 188.75 BOB1/ 110.78 B cell leukemia miR-34a-2/miR 110.9 OBF1 line (Karpas 231) 34a-1 04p15.3 D D4S1608 18.83 D4S404 23.98 5.15 primary bladder miR-218-1 20.25 ca. 05q31-33 D D5S1480 144.17 D5S820 156.1 11.93 prostate ca. miR-145/miR- 148.7 aggressiveness 143 05q32 D ADRB2 148.23 ATX1 151.15 2.92 myelodysplastic miR-145/miR- 148.7 syndrome 143 07q32 D D7S3061 122.84 D7S1804 131.25 8.41 prostate ca. miR-129-1; miR- 127.3; (aggressiveness) 182s/miR- 129; 130 182as/miR- 96/miR-183; miR29a/miR-29b 07q32-q33 D D7S2531 130.35 D7S1804 131.69 1.34 prostate ca. miR-29a/miR- 130 (aggressiveness) 29b 08p21 D (MRL1) D8S560 21.61 D8S1820 28.02 6.41 HCC miR-161; miR- 22; 21.5 177 08p21 D D8S282 21.42 0.1 HCC miR-177 21.5 08p22 D D8S254 16.62 SFTP2 22.05 5.43 oral and miR-161; miR- 22; 21.5 laryngeal 177 squamous carcinoma. 08p23.1 A D8S1819 6.737 D8S550 10.919 4.18 malignant miR-124a-1 9.75 fibrous histiocytomas (MFHs) 09p21 D (LOH) IFNA 21.2 D9S171/ 22.07 0.87 primary bladder miR-31 21.4 S1814 tumor 09p21 D IFNA 21.5 0 lung miR-31 21.4 adenocarcinoma 09p21 D IFNA 21.5 0 gastric ca. miR-31 21.4 09p21 D CDKN2A, 21.9 0.5 breast ca. miR-31 21.4 CDKN2B 09q22 D D9S280 92.47 D9S1809 93.93 1.46 urothelial ca. miR-24-1/miR- 92.9; 92.3 27b/miR-23b; let-7a-1/let- 7f1/let-7d 09q22.3 D (reg B) D9S12 91.21 D9S180 R 96.03 4.82 bladder ca. let-7a-1/let- 92.3; 92.9 7f1/let-7d; miR- 24-1/miR- 27b/miR-23b 09q32 D D9S1677 107.35 0.2 Small Cell Lung miR-32 107.15 Ca., Non-Small Cell Lung Ca. 09q33 D D9S1826 133.88 D9S158 134.53 0.4 NSCLC miR-123 134.95 09q33-34.1 D (reg D) GSN 119.45 D9S260 127.09 7.64 bladder ca. miR-181a; miR- 122.85; 199b 126.3 09q34 D D9S158 134.54 0.4 HCC miR-123 134.95 11p15 D D11S2071 0.23 0.4 ovarian ca. miR-210 0.6 11p15.5 D (LOH11B) HRAS 0.52 D11S1363 1.05 0.53 lung ca. miR-210 0.6 11q13 D D11S4946 64.35 D11S4939 64.54 0.19 sporadic miR-159-1/miR- 64.45 follicular thyroid 192 tumor 11q22 D D11S940/ 100.65 CD3D/ 118.7 18.05 lung miR-34a-1/miR- 111 S1782 D11S4104 adenocarcinoma 34a-2 11q22.1-23.2 D (MDR3) D11S2017 107.05 D11S965 111.3 4.25 nasopharyngeal miR-34a-1/miR- 111 carcinoma 34a-2 11q22.3-q25 D D11S1340 116.12 D11S912 128.16 12.04 ovarian ca. miR125b-1/let- 121.5 7a-2/miR-100 11q22-q23 D D11S2106/ 108.76 D11S1356 117.454 8.7 chronic miR-34a-1/miR- 111 S2220 lymphocytic 34a-2 leukemia 11q23 D D11S1647 110.34 NCAM2/ 112.5 2.16 lung ca. miR-34a-1/miR- 111 NCAM1 34a-2 11q23 D D11S1345 121.83 D11S1328 123.56 1.73 lung miR125b-1/let- 121.5 adenocarcinoma 7a-2/miR-100 11q23 D D11S1345 121.83 D11S1328 123.56 1.73 lung miR125b-1/let- 121.5 adenocarcinoma 7a-2/miR-100 11q23.1-23.2 D (LOH) D11S4167 121.68 D11S4144 122.96 1.28 cervical ca. miR125b-1/let- 121.5 7a-2/miR-100 11q23-q24 D D11S927 109.676 D11S1347 111.67 1.994 breast, lung ca. miR-34a-1/miR- 111 (LOH11CR1) 34a-2 11q23-q24 D D11S1345 121.835 D11S1328 123.56 1.725 breast, lung, miR125b-1/let- 121.5 (LOH11CR2) ovary, cervix ca. 7a-2/miR-100 12p13 t(7; 12)(q36; p13) TEL(ETV6) 11.83 near HLXB9 156.21 acute myeloid miR-153-2 156.6 leukemia (AML) 12q13-q14 A DGKA 54.6 BLOV1 67.4 12.8 adenocarcinomas let-7i 61.35 of lung and esophagus 12q13-q15 A GLI 56.15 MDM2 67.5 11.35 bladder ca. let-7i 61.3-.45 12q22 D D12S1716 95.45 P382A8AG/ 97.47 2.02 male germ cell miR-135-2 96.5 D12S296 tumors 12q22 D D12S377/ 94.1 D12S296 97.47 3.37 male germ cell miR-135-2 96.5 D12S101 tumors. 13q14.3 D D13S319/ 48.5 D13S25 49.04 0.54 B-Chronic miR-15a/miR- 48.5 D13S272 Lymphocytic 16a Leuk (B-CLL) 13q14 D D13S260 30.23 AFMa301wb5 48.62 18.39 adult miR-15a/miR- 48.5 Lymphoblastic 16a leukemia 13q14 D Rb1 46.77 BCMS 48.46 1.69 lipoma miR-15a/miR16a 48.5 (DLEU-1) 13q14.3 D (RMD) D13S272 48.5 AF077401 48.765 0.265 CLL miR-15a/miR- 48.5 16a 13q14.3 D (Reg II) D13S153 46.68 D13S1289 62.43 15.75 head-and-neck miR-15a/miR- 48.5 squamous-cell 16a carcinoma 13q14.3 D D13S273 48.11 D13S176 58.31 10.2 oral ca. miR-15a/miR- 48.5 16a 13q14.3 D D13S1168 48.28 D13S25 49.04 0.76 B-CLL miR-15a/miR- 48.5 16a 13q32-33 A stSG15303 89.7 stSG31624 96.85 7.15 follicular miR-17/miR- 89.7 Lymphoma 18/miR-19a/miR- 20/miR-19b- 1/miR-92-1 14q11.1-q12 D D14S283 20.67 D14S64 22.55 1.88 malignant miR-208 21.8 mesothelioma 14q32 D D14S51 95.56 telomere 105.2 9.64 nasopharyngeal miR-127/miR- 99.3; 99.5; carcinoma 136; miR- 102.5 154/miR- 134/miR-299; miR-203 15q11.1-15 D D15S128 22.67 D15S1012 36.72 14.05 malignant miR-211 29 mesothelioma. 17p11.2 A PNMT 17.351 0.5 breast ca miR-33b 17.8 17p11.2 D D17S1857 16.61 D17S805/ 20.79 4.18 kidney ca (Birt- miR-33b 17.9 S959 Hogg-Dube sy) 17p11.2 D D117S1857 16.61 D17S805/ 20.79 4.18 medulloblastoma miR-33b 17.9 S959 (Smith-Magenis syndrome) 17p13 D D17S578 7.025 0 HCC miR-195 7 17p13.3 D D17S1866 0.121 D17S1574 2.02 1.9 HCC miR-22; miR- 1.75; 2.2 132; miR-212 17p13.3 D ENO3 5.5 TP53 7.775 2.275 lung ca. miR-195 7 17p13.3 D D17S1574 2.02 D17S379 2.46 0.44 lung ca. miR-132; miR- 2.2 212 17q11.1 D NF1 29.7 0.3 ovarian ca. miR-108-1 30 17q11.1 D NF1 29.7 0.3 ovarian ca. miR-193 30 17q11.2 A MLN 62 27.22 0.1 primary breast miR-144 27.35 (TRAF4) ca. 17q11.2 D (NF1 locus) CYTOR4 29.25 WI-12393 30.52 1.27 NF1 miR-108-1/miR- 30; 30 microdeletion 193 17q22 t(8; 17) “BCL3” 56.95 c-MYC 128.7 prolymphocytic miR-142s/miR- 56.95 leukemia 142as 17q23 A RAD51C 57.116 0.25 breast ca. miR-142s/miR- 56.95 142as 17q23 A RAD51C 57.116 0.5 breast ca. miR-301 57.7 17q23 A CLTC 58.21 PPM1D 59.18 0.97 neuroblastoma miR-21 58.45 17q25 A (SRO2) D17S1306 53.76 D17S1604 58.45 4.69 breast ca. miR-142s; miR- 56.95; 142as; miR-301; 57.7; miR-21 58.45 19p13.3 D D19S886 0.95 D19S216 4.9 3.95 lung miR-7-3 4.75 adenocarcinoma 19p13.3 D (LOH) D19S216 4.9 D19S549 5.44 0.54 gynecological miR-7-3 4.75 tumor in Peutz- Jegher's sy 19p13.3 D (HZYG) D19S894 4.34 D19S395 7.32 2.98 gynecological miR-7-3 4.75 tumor in Peutz- Jegher's sy 19p13.3 D (LOH) D19S886 0.95 D19S216 4.9 3.95 pancreatic and miR-7-3 4.75 biliary ca 20q13 A FLJ33887 52.2 ZNF217 52.75 0.55 colon ca miR-297-3 52.35 20q13.1 A ZNF217 52.285 0 ovarian miR-297-3 52.35 20q13.2 A D20S854 52.68 D20S120 53.69 1.01 gastric miR-297-3 52.35 adenocarcinoma 20q13.2 A ZNF217 52.85 0.5 head/neck miR-297-3 52.35 squamous carcinoma 21q11.1 D D21S120/ 15.06 ANA 17.9 2.84 lung ca. (cell line miR-99a/let- 16.8 S1911 MA17) 7c/miR-125b-2 21q21 A BIC 25.8 BIC 25.9 0.1 colon ca. miR-155(BIC) 25.85 22q12.2-q13.33 D D22S280 31.53 D22S274 43.54 12.01 colorectal ca. miR-33a 40.6 22q12.3-q13.33 D D22S280 31.53 D22S282 42.1 10.57 astrocytomas miR-33a 40.6 22q12.1 t(4; 22) MN1 26.5 meningioma miR-180 26.45 Xq25-26.1 D DXS1206 125.08 HPRT 132.31 7.23 advanced miR-92-2/miR- 132 ovarian ca. 19b-2/miR-106a Note: D—deletion; A—amplification; ca.—cancer; sy—syndrome. The distance (in Mb) from the markers used in genome-wide analysis is shown. miRs in clusters are separated by a slash. Positions are according to BUILD 34, version 1, of the Human Genome

Example 4B Effect of Genomic Location on miR Gene Expression

In order to investigate whether the genomic location in deleted regions influences miR gene expression, a set of lung cancer cell lines was analyzed. miR-26a and miR-99a, located at 3p21 and 21q1.2, respectively, are not expressed or are expressed at low levels in lung cancer cell lines. The locations of miR-26a and miR-99a correlate with regions of LOH/HD in lung tumors. However, the expression of miR-16a (located at 13q14) was unchanged in the majority of lung tumor cell lines as compared to normal lung (see FIG. 1).

Several miR genes are located near breakpoint regions, including miR-142s at 50 nt from the t(8;17) translocation involving chromosome 17 and MYC, and miR-180 at 1 kb from the MN1 gene involved in a t(4;22) translocation in meningioma (Table 6). The t(8;17) translocation brings the MYC gene near the miR gene promoter, with consequent MYC over-expression, while the t(4;22) translocation inactivates the MN1 gene, and possibly inactivates the miR gene located in the same position. Other miR genes are located relatively close to chromosomal breakpoints, such as the cluster miR 34a-1/34a-2 and miR-153-2 (see Table 7). Further supporting a role for miR-122a in cancer, it was found herein that human miR-122a is located in the minimal amplicon around MALT1 in aggressive marginal zone lymphoma (MZL), and was found to be about 160 kb from the breakpoint region of translocation t(11;18) in mucosa-associated lymphoid tissue (MALT) lymphoma (Sanchez-Izquierdo et al., 2003, Blood 101:4539-4546). Apart from miR-122a, several other miR genes were located in regions particularly prone to cancer-specific abnormalities, such as miR-142s and miR-142 as, located at 17q23 close to a t(8;17) breakpoint in B cell acute leukemia, and also located within the minimal amplicon in breast cancer and near the FRA17B site, which is also a target for HPV16 integration in cervical tumors (see Tables 5 and 7).

Example 5 MicroRNAs are Located in or Near HOX Gene Clusters

Homeobox-containing genes are a family of transcription factor genes that play crucial roles during normal development and in oncogenesis. HOXB4, HOXB5, HOXC9, HOXC10, HOXD4 and HOXD8, all with miR gene neighbors, are deregulated in a variety of solid and hematopoietic cancers (Cillo et al., 1999, Exp. Cell Res. 248:1-9; Owebs et al., 2002, Stem Cells 20:364-379). A strong correlation was found between the location of specific miR genes and homeobox (HOX) genes. The miR-10a and miR-196-1 genes are located within the HOX B cluster on 17q21, while miR-196-2 is within the HOX C cluster at 12q13, and miR-10b maps to the HOX D cluster at 2q31 (see FIG. 2). Moreover, three other miRs (miR-148, miR-152 and miR-148b) are close to HOX clusters (less than 1 Mb; see FIG. 2). The 1 Mb distance was selected because some form of long-range coordinated regulation of gene expression was shown to expand up to one megabase to HOX clusters (Kamath et al., 2003, Nature 421:231-7). Such proximity of miR genes to HOX gene clusters is unlikely to have occurred by chance (IRR=15.77; p<0.001) (Table 4). Because collinear expression of, and cooperation between, HOX genes is well demonstrated, these data indicated that miRs are altered along with the HOX genes in human cancers.

Next, it was determined whether miR genes were located within class II HOX gene clusters as well. Fourteen additional human HOX gene clusters (Pollard et al., 2000, Current Biology 10:1059-1062) were analyzed, and seven miR genes (miR-129-1, miR-153-2, let-7a-1, let-7f-1, let-7d, miR-202 and miR-139) were located within 0.5 Mb of class II homeotic genes, a result which was highly unlikely to occur by chance (IRR=2.95, p<0.001) (Table 4).

Example 6 Expression of miR Gene Products in Human Cells

The cDNA sequence encoding the entire miR precursor transcript of an miR gene is separately cloned into the context of an irrelevant mRNA expressed under the control of the cytomegalovirus immediate early (CMV-IE) promoter, according to the procedure of Zeng et al., 2002, Mol. Cell. 9:1327-1333, the entire disclosure of which is herein incorporated by reference.

Briefly, Xho I linkers are placed on the end of double-stranded cDNA sequences encoding an miR precursor, and this construct is separately cloned into the Xho I site present in the pBC12/CMV plasmid. The pBC12/CMV plasmid is described in Cullen, 1986, Cell 46:973-982, the entire disclosure of which is herein incorporated by reference.

pCMV plasmid containing the miR precursor coding sequence is transfected into cultured human 293T cells by standard techniques using the FuGene 6 reagent (Roche). Total RNA is extracted as described above, and the presence of the processed miR transcript is detected by Northern blot analysis with an miR probe specific for the miR transcript.

pCMV-miR is also transfected into cultured human normal cells or cells with proliferative disorders, such as cancer cells. For example, the proliferative disease or cancer cell types include ovarian cancer, breast cancer, small cell lung cancer, sporadic follicular thyroid tumor, chronic lymphocytic leukemia, cervical cancer, acute myeloid leukemia, adenocarcinomas, male germ cell tumor, non-small cell lung cancer, gastric cancer, hepatocellular carcinoma, lung cancer, nasopharyngeal cancer, B-chronic lymphocytic leukemia, lipoma, mesothelioma, kidney cancer, NF1 microdeletion, neuroblastoma, medulloblastoma, pancreatic cancer, biliary cancer, colon cancer, gastric adenocarcinoma, head/neck squamous carcinoma, astrocytoma, meningioma, B cell leukemia, primary bladder cancer, prostate cancer, myelodysplastic syndrome, oral cavity carcinoma, laryngeal squamous carcinoma, and urothelial cancer. Total RNA is extracted as described above, and the presence of processed miR transcripts in the cancer cells is detected by Northern blot analysis with miR specific probes. The transfected cells are also evaluated for changes in morphology, the ability to overcome contact inhibition, and other markers indicative of a transformed phenotype.

Example 7 Preparation of Liposomes Encapsulating MiR Gene Products

Liposome Preparation 1—Liposomes composed of lactosyl cerebroside, phosphatidylglycerol, phosphatidylcholine, and cholesterol in molar ratios of 1:1:4:5 are prepared by the reverse phase evaporation method described in U.S. Pat. No. 4,235,871, the entire disclosure of which is herein incorporated by reference. The liposomes are prepared in an aqueous solution of 100 μg/ml processed miR transcripts or 500 μg/ml pCMV-microRNA. The liposomes thus prepared encapsulate either the processed microRNA, or the pCMV-microRNA plasmids.

The liposomes are then passed through a 0.4 polycarbonate membrane and suspended in saline, and are separated from non-encapsulated material by column chromatography in 135 mM sodium chloride, 10 mM sodium phosphate (pH 7.4). The liposomes are used without further modification, or are modified as described herein.

A quantity of the liposomes prepared above are charged to an appropriate reaction vessel to which is added, with stirring, a solution of 20 mM sodium metaperiodate, 135 mM sodium chloride and 10 mM sodium phosphate (pH 7.4). The resulting mixture is allowed to stand in darkness for 90 minutes at a temperature of about 20° C. Excess periodate is removed by dialysis of the reaction mixture against 250 ml of buffered saline (135 mM sodium chloride, 10 mM sodium phosphate, pH 7.4) for 2 hours. The product is a liposome having a surface modified by oxidation of carbohydrate hydroxyl groups to aldehyde groups. Targeting groups or opsonization inhibiting moieties are conjugated to the liposome surface via these aldehyde groups.

Liposome Preparation 2—A second liposome preparation composed of maleimidobenzoyl-phosphatidylethanolamine (MBPE), phosphatidylcholine and cholesterol is obtained as follows. MBPE is an activated phospholipid for coupling sulfhydryl-containing compounds, including proteins, to the liposomes.

Dimyristoylphosphatidylethanolamine (DMPE) (100 mmoles) is dissolved in 5 ml of anhydrous methanol containing 2 equivalents of triethylamine and 50 mg of m-maleimidobenzoyl N-hydroxysuccinimide ester, as described in Kitagawa et al. (1976), J. Biochem. 79:233-236, the entire disclosure of which is herein incorporated by reference. The resulting reaction is allowed to proceed under a nitrogen gas atmosphere overnight at room temperature, and is subjected to thin layer chromatography on Silica gel H in chloroform/methanol/water (65/25/4), which reveals quantitative conversion of the DMPE to a faster migrating product. Methanol is removed under reduced pressure and the products re-dissolved in chloroform. The chloroform phase is extracted twice with 1% sodium chloride and the maleimidobenzoyl-phosphatidylethanolamine (MBPE) purified by silicic acid chromatography with chloroform/methanol (4/1) as the solvent. Following purification, thin-layer chromatography indicates a single phosphate containing spot that is ninhydrin negative.

Liposomes are prepared with MBPE, phosphatidylcholine and cholesterol in molar ratios of 1:9:8 by the reverse phase evaporation method of U.S. Pat. No. 4,235,871, supra, in an aqueous solution of 100 μg/ml processed microRNA or a solution of 500 μg/ml pCMV-miR (see above). Liposomes are separated from non-encapsulated material by column chromatography in 100 mM sodium chloride-2 mM sodium phosphate (pH 6.0).

Example 8 Attachment of Anti-Tumor Antibodies to Liposomes

An appropriate vessel is charged with 1.1 ml (containing about 10 mmoles) of Liposome Preparation 1 (see above) carrying reactive aldehyde groups, or Liposome Preparation 2 (see above). 0.2 ml of a 200 mM sodium cyanoborohydride solution and 1.0 ml of a 3 mg/ml solution of a monoclonal antibody directed against a tumor cell antigen is added to the preparation, with stirring. The resulting reaction mixture is allowed to stand overnight while maintained at a temperature of 4° C. The reaction mixture is separated on a Biogel A5M agarose column (Biorad, Richmond, Calif.; 1.5×37 cm).

Example 9 Inhibition of Human Tumor Growth In Vivo with miR Gene Products

A cancer cell line, such as one of the lung cancer cell lines described above or a tumor-derived cell, is inoculated into nude mice, and the mice are divided into treatment and control groups. When tumors in the mice reach 100 to 250 cubic millimeters, processed miR transcripts encapsulated in liposomes are injected directly into the tumors of the test group. The tumors of the control group are injected with liposomes encapsulating carrier solution only. Tumor volume is measured throughout the study.

Example 10 Oligonucleotide Microchip for Genome-wide miRNA Profiling Introduction

A micro-chip microarray was prepared as follows, containing 368 gene-specific oligonucleotide probes generated from 248 miRNAs (161 human, 84 mouse, and 3 arabidopsis) and 15 tRNAs (8 human and 7 mouse). These sequences correspond to human and mouse miRNAs found in the miRNA Registry (June 2003) (Griffiths-Jones, S. (2004) Nucleic Acids Res. 32, D109-D111) or collected from published literature (Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. (2001) Science 294, 853-858; Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. & Bartel, D. P. (2003) Science 299, 1540; Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M. & Dreyfuss, G. (2002) Genes Dev 16, 720-728). For 76 miRNAs, two different oligonucleotide probes were designed, one containing the active sequence and the other specific for the precursor. Using these distinct sequences, we were able to separately analyze the expression of miRNA and pre-miRNA transcripts for the same gene.

Various specificity controls were used to validate data. For intra-assay validation, individual oligonucleotide-probes were printed in triplicate. Fourteen oligonucleotides had a total of six replicates because of identical mouse and human sequences and therefore were spotted on both human and mouse sections of the array.

Several mouse and human orthologs differ only in few bases, serving as controls for the hybridization stringency conditions. tRNAs from both species were also printed on the microchip, providing an internal, relatively stable positive, control for specific hybridization, while Arabidopsis sequences were selected, based on the absence of any homology with known miRNAs from other species, and used as controls for non-specific hybridization.

Materials and Methods

The following materials and methods were employed in designing and testing the microchip.

miRNA Oligonucleotide Probe Design. A total of 281 miRNA precursor sequences (190 Homo sapiens, 88 Mus musculus, and 3 Arabidopsis thaliana) with annotated active sites were selected for oligonucleotide design. These correspond to human and mouse miRNAs found in the miRNA Registry or collected from published literature. All of the sequences were confirmed by BLAST alignment with the corresponding genome and the hairpin structures were analyzed. When two precursors with different length or slightly different base composition for the same miRNAs were found, both sequences were included in the database and the one that satisfied the highest number of design criteria was used. The sequences were clustered by organism using the LEADS platform (Sorek, R., Ast, G. & Graur, D. (2002) Genome Research 12, 1060-1067), resulting in 248 clusters (84 mouse, 161 human, and 3 arabidopsis). For each cluster, all 40-mer oligonucleotides were evaluated for their cross-homology to all genes of the relevant organism, number of bases in alignment to a repetitive element, amount of low-complexity sequence, maximum homopolymeric stretch, global and local G+C content, and potential hairpins (self 5-mers). The best oligonucleotide was selected that contained each active site of each miRNA. This produced a total of 259 oligonucleotides; there were 11 clusters with multiple annotated active sites. Next, we attempted to design an oligonucleotide that did not contain the active site for each cluster, when it was possible to choose such an oligonucleotide that did not overlap the selected oligonucleotide(s) by more than 10 nt. To design each of these additional oligonucleotides, we required <75% global cross-homology and <20 bases in any 100% alignment to the relevant organism, <16 bases in alignments to repetitive elements, <16 bases of low-complexity, homopolymeric stretches of no more than 6 bases, G+C content between 30-70% and no more than 11 windows of size 10 with G+C content outside 30-70%, and no self 5-mers. A total of 76 additional oligonucleotides were designed. In addition, we designed oligonucleotides for 7 mouse tRNAs and 8 human tRNAs, using similar design criteria. We selected a single oligonucleotide for each, with the exception of the human and mouse initiators, Met-tRNA-i, for which we selected two oligonucleotides each (Table 8).

TABLE 8 Oligonucleotides used for the miRNA microarray chip and correspondence with specific human and mouse microRNAs. Covers SEQ Corresponding active   ID Oligonucleotide_name miRNA Oligonucleotide sequence site? Notes NO. ath-miR156a-#1 ath-miR156a TGACAGAAGAGAGTGAGCACACAAAGGCAATTTGCATATC yes 286 ath-miR156a-#2 ath-miR156a CATTGCACTTGCTTCTCTTGCGTGCTCACTGCTCTTTCTG no 287 ath-miR157a-#1 ath-miR157a GTGTTGACAGAAGATAGAGAGCACAGATGATGAGATACAA yes 288 ath-miR157a-#2 ath-miR157a CATCTTACTCCTTTGTGCTCTCTAGCCTTCTGTCATCACC no 289 ath-miR180a-#1 ath-miR180 GATGGACGGTGGTGATTCACTCTCCACAAAGTTCTCTATG no 290 ath-miR180a-#2 ath-miR180 TGAGAATCTTGATGATGCTGCATCGGCAATCAACGACTAT yes 291 hsa-let-7a-1-prec let-7a-1 TGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCA yes 292 hsa-let-7a-2-prec-#1 let-7a-2 TACAGCCTCCTAGCTTTCCTTGGGTCTTGCACTAAACAAC no 293 hsa-let-7a-2-prec-#2 let-7a-2 ACTGCATGCTCCCAGGTTGAGGTAGTAGGTTGTATAGTTT yes 294 hsa-let-7a-3-prec let-7a-3 GGGTGAGGTAGTAGGTTGTATAGTTTGGGGCTCTGCCCTG yes 295 hsa-let-7b-prec let-7b TGAGGTAGTAGGTTGTGTGGTTTCAGGGCAGTGATGTTGC yes 296 hsa-let-7c-prec let-7c GCATCCGGGTTGAGGTAGTAGGTTGTATGGTTTAGAGTTA yes 297 hsa-let-7d-prec let-7d CCTAGGAAGAGGTAGTAGGTTGCATAGTTTTAGGGCAGGG yes 298 hsa-let-7d-v1-prec let-7d  CTAGGAAGAGGTAGTAGTTTGCATAGTTTTAGGGCAAAGA yes 299 (= 7d-v1) hsa-let-7d-v2-prec-#1 let-7i  TTGGTCGGGTTGTGACATTGCCCGCTGTGGAGATAACTGC no 300 (= let-7d-v2) hsa-let-7d-v2-prec-#2 let-7i  GCTGAGGTAGTAGTTTGTGCTGTTGGTCGGGTTGTGACAT yes idem mmu- 301 (= let-7d-v2) let-7i-prec hsa-let-7e-prec let-7e GGCTGAGGTAGGAGGTTGTATAGTTGAGGAGGACACCCAA yes 302 hsa-let-7f-1-prec-#1 let-7f-1 GGTAGTGATTTTACCCTGTTCAGGAGATAACTATACAATC no 303 hsa-let-7f-1-prec-#2 let-7f-1 GGGATGAGGTAGTAGATTGTATAGTTGTGGGGTAGTGATT yes 304 hsa-let-7f-2-prec2 let-7f-2 TGAGGTAGTAGATTGTATAGTTTTAGGGTCATACCCCATC yes 305 hsa-let-7g-prec-#1 let-7g CTGATTCCAGGCTGAGGTAGTAGTTTGTACAGTTTGAGGG yes 306 hsa-let-7g-prec-#2 let-7g TTGAGGGTCTATGATACCACCCGGTACAGGAGATAACTGT no 307 hsa-miR-001b-1-prec1 miR-001 AATGCTATGGAATGTAAAGAAGTATGTATTTTTGGTAGGC yes 308 hsa-miR-001b-2-prec miR-001 TAAGCTATGGAATGTAAAGAAGTATGTATCTCAGGCCGGG yes 309 hsa-miR-007-1-prec miR-007-1 TGTTGGCCTAGTTCTGTGTGGAAGACTAGTGATTTTGTTG yes 310 hsa-miR-007-2-prec-#1 miR-007-2 TACTGCGCTCAACAACAAATCCCAGTCTACCTAATGGTGC no 311 hsa-miR-007-2-prec-#2 miR-007-2 GGACCGGCTGGCCCCATCTGGAAGACTAGTGATTTTGTTG yes 312 hsa-miR-007-3-prec-#1 miR-007-3 AGATTAGAGTGGCTGTGGTCTAGTGCTGTGTGGAAGACTA no 313 hsa-miR-007-3-prec-#2 miR-007-3 TGGAAGACTAGTGATTTTGTTGTTCTGATGTACTACGACA yes 314 hsa-miR-009-1-#1 miR-009-1 TCTTTGGTTATCTAGCTGTATGAGTGGTGTGGAGTCTTCA yes 315 (miR-131-1) hsa-miR-009-1-#2 miR-009-1 TAAAGCTAGATAACCGAAAGTAAAAATAACCCCATACACT yes 316 (miR-131-1) hsa-miR-009-2-#1 miR-009-2 GAAGCGAGTTGTTATCTTTGGTTATCTAGCTGTATGAGTG yes 317 (miR-131-2) hsa-miR-009-2-#2 miR-009-2 GAGTGTATTGGTCTTCATAAAGCTAGATAACCGAAAGTAA yes idem mmu- 318 (miR-131-2) miR-009- prec-#2 hsa-miR-009-3-#1 miR-009-3 GGGAGGCCCGTTTCTCTCTTTGGTTATCTAGCTGTATGAG yes 319 (miR-131-3) hsa-miR-009-3-#2 miR-009-3 GTGCCACAGAGCCGTCATAAAGCTAGATAACCGAAAGTAG yes 320 (miR-131-3) hsa-miR-010a-prec-#1 miR-010a GTCTGTCTTCTGTATATACCCTGTAGATCCGAATTTGTGT yes 321 hsa-miR-010a-prec-#2 miR-010a GTGGTCACAAATTCGTATCTAGGGGAATATGTAGTTGACA no 322 hsa-miR-010b-prec-#1 miR-010b TACCCTGTAGAACCGAATTTGTGTGGTATCCGTATAGTCA yes 323 hsa-miR-010b-prec-#2 miR-010b GTCACAGATTCGATTCTAGGGGAATATATGGTCGATGCAA no 324 hsa-miR-015a-2-prec-#1 miR-15-a CCTTGGAGTAAAGTAGCAGCACATAATGGTTTGTGGATTT yes 325 hsa-miR-015a-2-prec-#2 miR-15-a TTTGTGGATTTTGAAAAGGTGCAGGCCATATTGTGCTGCC no 326 hsa-miR-015b-prec-#1 miR-015-b GGCCTTAAAGTACTGTAGCAGCACATCATGGTTTACATGC yes 327 hsa-miR-015b-prec-#2 miR-015-b TGCTACAGTCAAGATGCGAATCATTATTTGCTGCTCTAGA no 328 hsa-miR-016a-chr13 miR-016-1 CAATGTCAGCAGTGCCTTAGCAGCACGTAAATATTGGCGT yes 329 hsa-miR-016b-chr3 miR-016-2 GTTCCACTCTAGCAGCACGTAAATATTGGCGTAGTGAAAT yes 330 hsa-miR-017-prec-#1 miR-017 GCATCTACTGCAGTGAAGGCACTTGTAGCATTATGGTGAC yes 331 (miR-091) hsa-miR-017-prec-#2 miR-017 GTCAGAATAATGTCAAAGTGCTTACAGTGCAGGTAGTGAT yes 332 (miR-091) hsa-miR-018-prec miR-018 TAAGGTGCATCTAGTGCAGATAGTGAAGTAGATTAGCATC yes 333 hsa-miR-019a-prec miR-019a TGTAGTTGTGCAAATCTATGCAAAACTGATGGTGGCCTGC yes 334 hsa-miR-019b-1-prec miR-019b-1 TTCTGCTGTGCAAATCCATGCAAAACTGACTGTGGTAGTG yes 335 hsa-miR-019b-2-prec miR-019b-2 GTGGCTGTGCAAATCCATGCAAAACTGATTGTGATAATGT yes 336 hsa-miR-020-prec miR-020 TAAAGTGCTTATAGTGCAGGTAGTGTTTAGTTATCTACTG yes 337 hsa-miR-021-prec-17-#1 miR-021 GTCGGGTAGCTTATCAGACTGATGTTGACTGTTGAATCTC yes 338 hsa-miR-021-prec-17-#2 miR-021 TTCAACAGTCAACATCAGTCTGATAAGCTACCCGACAAGG yes 339 hsa-miR-022-prec miR-022 TGTCCTGACCCAGCTAAAGCTGCCAGTTGAAGAACTGTTG yes 340 hsa-miR-023a-prec miR-023a TCCTGTCACAAATCACATTGCCAGGGATTTCCAACCGACC yes 341 hsa-miR-023b-prec miR-023b AATCACATTGCCAGGGATTACCACGCAACCACGACCTTGG yes 342 hsa-miR-024-1-prec-#1 miR-024-1 TTTTACACACTGGCTCAGTTCAGCAGGAACAGGAGTCGAG yes 343 hsa-miR-024-1-prec-#2 miR-024-1 TCCGGTGCCTACTGAGCTGATATCAGTTCTCATTTTACAC yes 344 hsa-miR-024-2-prec miR-024-2 AGTTGGTTTGTGTACACTGGCTCAGTTCAGCAGGAACAGG yes 345 hsa-miR-025-prec miR-025 ACGCTGCCCTGGGCATTGCACTTGTCTCGGTCTGACAGTG yes 346 hsa-miR-026a-prec-#1 miR-026a TTCAAGTAATCCAGGATAGGCTGTGCAGGTCCCAATGGCC yes 347 hsa-miR-026a-prec-#2 miR-026a TCCCAATGGCCTATCTTGGTTACTTGCACGGGGACGCGGG no 348 hsa-miR-026b-prec miR-026b TTCAAGTAATTCAGGATAGGTTGTGTGCTGTCCAGCCTGT yes 349 hsa-miR-027a-prec miR-027a GTCCACACCAAGTCGTGTTCACAGTGGCTAAGTTCCGCCC yes 350 hsa-miR-027b-prec miR-027b CCGCTTTGTTCACAGTGGCTAAGTTCTGCACCTGAAGAGA yes 351 hsa-miR-028-prec miR-028 AAGGAGCTCACAGTCTATTGAGTTACCTTTCTGACTTTCC yes 352 hsa-miR-029a-2-#1 miR-029a CTAGCACCATCTGAAATCGGTTATAATGATTGGGGAAGAG yes 353 hsa-miR-029a-2-#2 miR-029a CCCCTTAGAGGATGACTGATTTCTTTTGGTGTTCAGAGTC no 354 hsa-miR-029b-2 = miR-029b AGTGATTGTCTAGCACCATTTGAAATCAGTGTTCTTGGGG yes 355 102prec7.1 = 7.2 (= miR-102- 7.1 = 7.2) hsa-miR-029c-prec miR-029c TTTTGTCTAGCACCATTTGAAATCGGTTATGATGTAGGGG yes 356 hsa-miR-030a-prec-#1 miR-030a-as GCGACTGTAAACATCCTCGACTGGAAGCTGTGAAGCCACA yes 357 hsa-miR-030a-prec-#2 miR-030a-s CACAGATGGGCTTTCAGTCGGATGTTTGCAGCTGCCTACT yes 358 hsa-miR-030b-prec-#1 miR-030b TGTAAACATCCTACACTCAGCTGTAATACATGGATTGGCT yes 359 hsa-miR-030b-prec-#2 miR-030b ATGGATTGGCTGGGAGGTGGATGTTTACTTCAGCTGACTT no 360 hsa-miR-030c-prec miR-030c TACTGTAAACATCCTACACTCTCAGCTGTGGAAAGTAAGA yes 361 hsa-miR-030d-prec-#1 miR-030d TAAGACACAGCTAAGCTTTCAGTCAGATGTTTGCTGCTAC no 362 hsa-miR-030d-prec-#2 miR-030d TTGTAAACATCCCCGACTGGAAGCTGTAAGACACAGCTAA yes 363 hsa-miR-031-prec miR-031 GGCAAGATGCTGGCATAGCTGTTGAACTGGGAACCTGCTA yes 364 hsa-miR-032-prec-#1 miR-032 TGTCACGGCCTCAATGCAATTTAGTGTGTGTGATATTTTC no 365 hsa-miR-032-prec-#2 miR-032 GGAGATATTGCACATTACTAAGTTGCATGTTGTCACGGCC yes 366 hsa-miR-033b-prec miR-033b GTGCATTGCTGTTGCATTGCACGTGTGTGAGGCGGGTGCA yes 367 hsa-miR-033-prec miR-33 GTGGTGCATTGTAGTTGCATTGCATGTTCTGGTGGTACCC yes 368 hsa-miR-034-prec-#1 miR-034 GAGTGTTTCTTTGGCAGTGTCTTAGCTGGTTGTTGTGAGC yes 369 (= miR-170) hsa-miR-034-prec-#2 miR-034 AGTAAGGAAGCAATCAGCAAGTATACTGCCCTAGAAGTGC no 370 (= miR-170) hsa-miR-092-prec- miR-092-1 ACAGGTTGGGATCGGTTGCAATGCTGTGTTTCTGTATGGT no 371 13 = 092-1-#1 hsa-miR-092-prec- miR-092-1 TCTGTATGGTATTGCACTTGTCCCGGCCTGTTGAGTTTGG yes 372 13 = 092-1-#2 hsa-miR-092-prec- miR-092-2 GTTCTATATAAAGTATTGCACTTGTCCCGGCCTGTGGAAG yes 373 X = 092-2 hsa-miR-093-prec- miR-093-1 CCAAAGTGCTGTTCGTGCAGGTAGTGTGATTACCCAACCT yes 374 7.1 = 093-1 hsa-miR-095-prec-4 miR-095 CGTTACATTCAACGGGTATTTATTGAGCACCCACTCTGTG yes 375 hsa-miR-096-prec-7-#1 miR-096 CTCCGCTCTGAGCAATCATGTGCAGTGCCAATATGGGAAA no 376 hsa-miR-096-prec-7-#2 miR-096 TGGCCGATTTTGGCACTAGCACATTTTTGCTTGTGTCTCT yes 377 hsa-miR-098-prec-X miR-098 TGAGGTAGTAAGTTGTATTGTTGTGGGGTAGGGATATTAG yes 378 hsa-miR-099b-prec-19- miR-099b GCCTTCGCCGCACACAAGCTCGTGTCTGTGGGTCCGTGTC no idem mmu- 379 #1 miR-099b- prec-#1 hsa-miR-099b-prec-19- miR-099b CACCCGTAGAACCGACCTTGCGGGGCCTTCGCCGCACACA yes idem mmu- 380 #2 miR-099b- prec-#2 hsa-miR-099-prec-21 miR-099a  ATAAACCCGTAGATCCGATCTTGTGGTGAAGTGGACCGCA yes 381 (= miR-099- prec21) hsa-miR-100-1/2-prec miR-100 TGAGGCCTGTTGCCACAAACCCGTAGATCCGAACTTGTGG yes 382 hsa-miR-101-1/2-prec-#1 miR-101-1 CCCTGGCTCAGTTATCACAGTGCTGATGCTGTCTATTCTA no 383 hsa-miR-101-1/2-prec-#2 miR-101-1 TACAGTACTGTGATAACTGAAGGATGGCAGCCATCTTACC yes 384 hsa-miR-101-prec-9 miR-101-2 GCTGTATATCTGAAAGGTACAGTACTGTGATAACTGAAGA yes 385 hsa-miR-102-prec-1 miR-102 TCTTTGTATCTAGCACCATTTGAAATCAGTGTTTTAGGAG yes 386 hsa-miR-103-2-prec miR-103-2 GTAGCATTCAGGTCAAGCAACATTGTACAGGGCTATGAAA yes 387 hsa-miR-103-prec- miR-103-1 TATGGATCAAGCAGCATTGTACAGGGCTATGAAGGCATTG yes 388 5 = 103-1 (= miR-103-5) hsa-miR-105-prec- miR-105-1 ATCGTGGTCAAATGCTCAGACTCCTGTGGTGGCTGCTCAT yes 389 X.1 = 105-1 (= miR-105- prec-X) hsa-miR-106-prec-X miR-106a CCTTGGCCATGTAAAAGTGCTTACAGTGCAGGTAGCTTTT yes 390 hsa-miR-107-prec-10 miR-107 GGCATGGAGTTCAAGCAGCATTGTACAGGGCTATCAAAGC yes 391 hsa-miR-122a-prec miR-122a CCTTAGCAGAGCTGTGGAGTGTGACAATGGTGTTTGTGTC yes 392 hsa-miR-123-prec-#1 miR-123 = GACGGGACATTATTACTTTTGGTACGCGCTGTGACACTTC yes 393 miR-126 hsa-miR-123-prec-#2 miR-123 = TGTGACACTTCAAACTCGTACCGTGAGTAATAATGCGCCG yes 394 miR-126 hsa-miR-124a-1-prec1 miR-124a-1 ATACAATTAAGGCACGCGGTGAATGCCAAGAATGGGGCTG yes 395 hsa-miR-124a-2-prec miR-124a-2 TTAAGGCACGCGGTGAATGCCAAGAGCGGAGCCTACGGCT yes 396 hsa-miR-124a-3-prec miR-124a-3 TTAAGGCACGCGGTGAATGCCAAGAGAGGCGCCTCCGCCG yes 397 hsa-miR-125a-prec-#1 miR-125a TCTAGGTCCCTGAGACCCTTTAACCTGTGAGGACATCCAG yes 398 hsa-miR-125a-prec-#2 miR-125a CAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGC no 399 hsa-miR-125b-1 miR-125b-1 TCCCTGAGACCCTAACTTGTGATGTTTACCGTTTAAATCC yes 400 hsa-miR-125b-2-prec-#1 miR-125b-2 TAGTAACATCACAAGTCAGGCTCTTGGGACCTAGGCGGAG no 401 hsa-miR-125b-2-prec-#2 miR-125b-2 ACCAGACTTTTCCTAGTCCCTGAGACCCTAACTTGTGAGG yes 402 hsa-miR-127-prec miR-127 TCGGATCCGTCTGAGCTTGGCTGGTCGGAAGTCTCATCAT yes 403 hsa-miR-128a-prec-#1 miR-128a TTGGATTCGGGGCCGTAGCACTGTCTGAGAGGTTTACATT no idem mmu- 404 miR-128- prec-#2 hsa-miR-128a-prec-#2 miR-128a ACATTTCTCACAGTGAACCGGTCTCTTTTTCAGCTGCTTC yes 405 hsa-miR-128b-prec-#1 miR-128b TCACAGTGAACCGGTCTCTTTCCCTACTGTGTCACACTCC yes 406 hsa-miR-128b-prec-#2 miR-128b GGGGGCCGATACACTGTACGAGAGTGAGTAGCAGGTCTCA no 407 hsa-miR-129-prec-#1 miR-129-1/2 TGGATCTTTTTGCGGTCTGGGCTTGCTGTTCCTCTCAACA yes 408 hsa-miR-129-prec-#2 miR-129-1/2 CCTCTCAACAGTAGTCAGGAAGCCCTTACCCCAAAAAGTA no 409 hsa-miR-130a-prec-#1 miR-130a CCAGAGCTCTTTTCACATTGTGCTACTGTCTGCACCTGTC no 410 hsa-miR-130a-prec-#2 miR-130a TGTCTGCACCTGTCACTAGCAGTGCAATGTTAAAAGGGCA yes 411 hsa-miR-132-prec-#1 miR-132 TGTGGGAACTGGAGGTAACAGTCTACAGCCATGGTCGCCC yes 412 hsa-miR-132-prec-#2 miR-132 TCCAGGGCAACCGTGGCTTTCGATTGTTACTGTGGGAACT no 413 hsa-miR-133a-1 miR-133a-1 CCTCTTCAATGGATTTGGTCCCCTTCAACCAGCTGTAGCT yes 414 (= miR-133c) hsa-miR-133a-2 miR-133a-2 TTGGTCCCCTTCAACCAGCTGTAGCTGTGCATTGATGGCG yes 415 (= miR-133d) hsa-miR-134-prec-#1 miR-134 ATGCACTGTGTTCACCCTGTGGGCCACCTAGTCACCAACC no 416 hsa-miR-134-prec-#2 miR-134 GTGTGTGACTGGTTGACCAGAGGGGCATGCACTGTGTTCA yes 417 hsa-miR-135-1-prec miR-135-1  GCCTCGCTGTTCTCTATGGCTTTTTATTCCTATGTGATTC yes 418 (= miR-135) hsa-miR-135-2-prec miR-135-2 CACTCTAGTGCTTTATGGCTTTTTATTCCTATGTGATAGT yes 419 hsa-miR-136-prec-#1 miR-136 ATGCTCCATCATCGTCTCAAATGAGTCTTCAGAGGGTTCT no 420 hsa-miR-136-prec-#2 miR-136 TGAGCCCTCGGAGGACTCCATTTGTTTTGATGATGGATTC yes 421 hsa-miR-137-prec miR-137 GGATTACGTTGTTATTGCTTAAGAATACGCGTAGTCGAGG yes idem mmu- 422 miR- 137-prec hsa-miR-138-1-prec miR-138-1 AGCTGGTGTTGTGAATCAGGCCGTTGCCAATCAGAGAACG yes 423 hsa-miR-138-2-prec miR-138-2 AGCTGGTGTTGTGAATCAGGCCGACGAGCAGCGCATCCTC yes idem mmu- 424 miR- 138-prec hsa-miR-139-prec miR-139 GTGTATTCTACAGTGCACGTGTCTCCAGTGTGGCTCGGAG yes 425 hsa-miR-140-#1 miR-140-as GCCAGTGGTTTTACCCTATGGTAGGTTACGTCATGCTGTT no 426 hsa-miR-140-#2 miR-140-as TTCTACCACAGGGTAGAACCACGGACAGGATACCGGGGCA yes 427 hsa-miR-141-prec-#1 miR-141 TTGTGAAGCTCCTAACACTGTCTGGTAAAGATGGCTCCCG yes 428 hsa-miR-141-prec-#2 miR-141 ATCTTCCAGTACAGTGTTGGATGGTCTAATTGTGAAGCTC no 429 hsa-miR-142-prec miR-142-as CCCATAAAGTAGAAAGCACTACTAACAGCACTGGAGGGTG yes idem mmu- 430 miR- 142-prec hsa-miR-143-prec miR-143 CTGGTCAGTTGGGAGTCTGAGATGAAGCACTGTAGCTCAG yes 431 hsa-miR-144-prec-#1 miR-144 CGATGAGACACTACAGTATAGATGATGTACTAGTCCGGGC yes 432 hsa-miR-144-prec-#2 miR-144 CCCTGGCTGGGATATCATCATATACTGTAAGTTTGCGATG no 433 hsa-miR-145-prec miR-145 CCTCACGGTCCAGTTTTCCCAGGAATCCCTTAGATGCTAA yes 434 hsa-miR-146-prec miR-146 TGAGAACTGAATTCCATGGGTTGTGTCAGTGTCAGACCTC yes 435 hsa-miR-147-prec miR-147 GACTATGGAAGCCAGTGTGTGGAAATGCTTCTGCTAGATT yes 436 hsa-miR-148-prec miR-148 TGAGTATGATAGAAGTCAGTGCACTACAGAACTTTGTCTC yes 437 hsa-miR-149-prec miR-149 CGAGCTCTGGCTCCGTGTCTTCACTCCCGTGCTTGTCCGA yes 438 hsa-miR-150-prec miR-150 CTCCCCATGGCCCTGTCTCCCAACCCTTGTACCAGTGCTG yes 439 hsa-miR-151-prec miR-151 GTATGTCTCATCCCCTACTAGACTGAAGCTCCTTGAGGAC yes 440 hsa-miR-152-prec-#1 miR-152 ACTCGGGCTCTGGAGCAGTCAGTGCATGACAGAACTTGGG yes idem mmu- 441 miR- 152-prec hsa-miR-152-prec-#2 miR-152 CCCCGGCCCAGGTTCTGTGATACACTCCGACTCGGGCTCT no 442 hsa-miR-153-1-prec1 miR-153-1 CAGTTGCATAGTCACAAAAGTGATCATTGGCAGGTGTGGC yes 443 hsa-miR-153-1-prec2 miR-153-1 CACAGCTGCCAGTGTCATTGTCACAAAAGTGATCATTGGC yes 444 hsa-miR-153-2-prec miR-153-2 GCCCAGTTGCATAGTCACAAAAGTGATCATTGGAAACTGT yes 445 hsa-miR-154-prec1-#1 miR-154 GTGGTACTTGAAGATAGGTTATCCGTGTTGCCTTCGCTTT yes 446 hsa-miR-154-prec1-#2 miR-154 GCCTTCGCTTTATTTGTGACGAATCATACACGGTTGACCT no 447 hsa-miR-155-prec miR-155(BIC) TTAATGCTAATCGTGATAGGGGTTTTTGCCTCCAACTGAC yes 448 hsa-miR-181a-prec-#1 miR-181a TCAGAGGACTCCAAGGAACATTCAACGCTGTCGGTGAGTT yes 449 (= miR-178-2) hsa-miR-181a-prec-#2 miR-181a GAAAAAACCACTGACCGTTGACTGTACCTTGGGGTCCTTA no 450 (= miR-178-2) hsa-miR-181b-prec-#1 miR-181b TGAGGTTGCTTCAGTGAACATTCAACGCTGTCGGTGAGTT yes 451 (= miR-178) hsa-miR-181b-prec-#2 miR-181b ACCATCGACCGTTGATTGTACCCTATGGCTAACCATCATC yes 452 (= miR-178) hsa-miR-181c-prec-#1 miR-181c TGCCAAGGGTTTGGGGGAACATTCAACCTGTCGGTGAGTT yes 453 hsa-miR-181c-prec-#2 miR-181c ATCGACCGTTGAGTGGACCCTGAGGCCTGGAATTGCCATC no 454 hsa-miR-182-prec-#1 miR-182-s AGGTAACAGGATCCGGTGGTTCTAGACTTGCCAACTATGG no 455 hsa-miR-182-prec-#2 miR-182-s TTGGCAATGGTAGAACTCACACTGGTGAGGTAACAGGATC yes 456 hsa-miR-183-prec-#1 miR-183 GACTCCTGTTCTGTGTATGGCACTGGTAGAATTCACTGTG yes 457 (= miR-174) hsa-miR-183-prec-#2 miR-183 GTCTCAGTCAGTGAATTACCGAAGGGCCATAAACAGAGCA no 458 (= miR-174) hsa-miR-184-prec-#1 miR-184 GACTGTAAGTGTTGGACGGAGAACTGATAAGGGTAGGTGA yes 459 hsa-miR-184-prec-#2 miR-184 CGTCCCCTTATCACTTTTCCAGCCCAGCTTTGTGACTGTA no 460 hsa-miR-185-prec-#1 miR-185 GCGAGGGATTGGAGAGAAAGGCAGTTCCTGATGGTCCCCT yes 461 hsa-miR-185-prec-#2 miR-185 CCTCCCCAGGGGCTGGCTTTCCTCTGGTCCTTCCCTCCCA no 462 hsa-miR-186-prec miR-186 CTTGTAACTTTCCAAAGAATTCTCCTTTTGGGCTTTCTGG yes 463 hsa-miR-187-prec-#1 miR-187 CTCGTGTCTTGTGTTGCAGCCGGAGGGACGCAGGTCCGCA yes 464 hsa-miR-187-prec-#2 miR-187 TCACCATGACACAGTGTGAGACTCGGGCTACAACACAGGA no 465 hsa-miR-188-prec miR-188 TCACATCCCTTGCATGGTGGAGGGTGAGCTTTCTGAAAAC yes 466 hsa-miR-190-prec miR-190 GCAGGCCTCTGTGTGATATGTTTGATATATTAGGTTGTTA yes 467 hsa-miR-191-prec miR-191 CAACGGAATCCCAAAAGCAGCTGTTGTCTCCAGAGCATTC yes idem mmu- 468 miR- 191-prec hsa-miR-192-2/3-#1 miR-192 TCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCT yes 469 hsa-miR-192-2/3-#2 miR-192 CCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAG no 470 hsa-miR-193-prec-#1 miR-193 AGATGAGGGTGTCGGATCAACTGGCCTACAAAGTCCCAGT yes 471 hsa-miR-193-prec-#2 miR-193 AGGATGGGAGCTGAGGGCTGGGTCTTTGCGGGCGAGATGA no 472 hsa-miR-194-prec-#1 miR-194 TGTAACAGCAACTCCATGTGGACTGTGTACCAATTTCCAG yes 473 hsa-miR-194-prec-#2 miR-194 CCAATTTCCAGTGGAGATGCTGTTACTTTTGATGGTTACC no 474 hsa-miR-195-prec miR-195 TCTAGCAGCACAGAAATATTGGCACAGGGAAGCGAGTCTG yes 475 hsa-miR-196-1-prec-#1 miR-196-1 CTGCTGAGTGAATTAGGTAGTTTCATGTTGTTGGGCCTGG yes 476 hsa-miR-196-1-prec-#2 miR-196-1 ACACAACAACATTAAACCACCCGATTCACGGCAGTTACTG no 477 hsa-miR-196-2-prec-#1 miR-196-2 AGAAACTGCCTGAGTTACATCAGTCGGTTTTCGTCGAGGG no 478 hsa-miR-196-2-prec-#2 miR-196-2 GCTGATCTGTGGCTTAGGTAGTTTCATGTTGTTGGGATTG yes 479 hsa-miR-197-prec miR-197 TAAGAGCTCTTCACCCTTCACCACCTTCTCCACCCAGCAT yes 480 hsa-miR-198-prec miR-198 TCATTGGTCCAGAGGGGAGATAGGTTCCTGTGATTTTTCC yes 481 hsa-miR-199a-1-prec miR-199a-1 GCCAACCCAGTGTTCAGACTACCTGTTCAGGAGGCTCTCA yes 482 (= 199s) hsa-miR-199a-2-prec miR-199a-2 TCGCCCCAGTGTTCAGACTACCTGTTCAGGACAATGCCGT yes 483 hsa-miR-199b-prec-#1 miR-199b GTCTGCACATTGGTTAGGCTGGGCTGGGTTAGACCCTCGG no 484 hsa-miR-199b-prec-#2 miR-199b ACCTCCACTCCGTCTACCCAGTGTTTAGACTATCTGTTCA yes 485 hsa-miR-200a-prec miR-200a GTCTCTAATACTGCCTGGTAATGATGACGGCGGAGCCCTG yes 486 hsa-miR-202-prec miR-202 GATCTGGCCTAAAGAGGTATAGGGCATGGGAAGATGGAGC yes 487 hsa-miR-203-prec-#1 miR-203 GTTCTGTAGCGCAATTGTGAAATGTTTAGGACCACTAGAC yes 488 hsa-miR-203-prec-#2 miR-203 TGGGTCCAGTGGTTCTTAACAGTTCAACAGTTCTGTAGCG no 489 hsa-miR-204-prec-#1 miR-204 CGTGGACTTCCCTTTGTCATCCTATGCCTGAGAATATATG yes 490 hsa-miR-204-prec-#2 miR-204 AGGCTGGGAAGGCAAAGGGACGTTCAATTGTCATCACTGG no 491 hsa-miR-205-prec miR-205 TCCTTCATTCCACCGGAGTCTGTCTCATACCCAACCAGAT yes 492 hsa-miR-206-prec-#1 miR-206 TTGCTATGGAATGTAAGGAAGTGTGTGGTTTCGGCAAGTG yes 493 hsa-miR-206-prec-#2 miR-206 TGCTTCCCGAGGCCACATGCTTCTTTATATCCCCATATGG no 494 hsa-miR-208-prec miR-208 ACCTGATGCTCACGTATAAGACGAGCAAAAAGCTTGTTGG yes 495 hsa-miR-210-prec miR-210 AGACCCACTGTGCGTGTGACAGCGGCTGATCTGTGCCTGG yes 496 hsa-miR-211-prec-#1 miR-211 TTCCCTTTGTCATCCTTCGCCTAGGGCTCTGAGCAGGGCA yes 497 hsa-miR-211-prec-#2 miR-211 GCAGGGACAGCAAAGGGGTGCTCAGTTGTCACTTCCCACA no 498 hsa-miR-212-prec-#1 miR-212 CCTCAGTAACAGTCTCCAGTCACGGCCACCGACGCCTGGC yes 499 hsa-miR-212-prec-#2 miR-212 CGGACAGCGCGCCGGCACCTTGGCTCTAGACTGCTTACTG no 500 hsa-miR-213-prec-#1 miR-213 AACATTCATTGCTGTCGGTGGGTTGAACTGTGTGGACAAG yes idem mmu- 501 miR- 213-prec hsa-miR-213-prec-#2 miR-213 TGTGGACAAGCTCACTGAACAATGAATGCAACTGTGGCCC no 502 hsa-miR-214-prec miR-214 TGTACAGCAGGCACAGACAGGCAGTCACATGACAACCCAG yes idem mmu- 503 miR- 214-prec hsa-miR-215-prec-#1 miR-215 CAGGAAAATGACCTATGAATTGACAGACAATATAGCTGAG yes 504 hsa-miR-215-prec-#2 miR-215 CATTTCTTTAGGCCAATATTCTGTATGACTGTGCTACTTC no 505 hsa-miR-216-prec-#1 miR-216 CTGGGATTATGCTAAACAGAGCAATTTCCTAGCCCTCACG no 506 hsa-miR-216-prec-#2 miR-216 GATGGCTGTGAGTTGGCTTAATCTCAGCTGGCAACTGTGA yes 507 hsa-miR-217-prec-#1 miR-217 GAATCAGTCACCATCAGTTCCTAATGCATTGCCTTCAGCA no 508 hsa-miR-217-prec-#2 miR-217 TGTCGCAGATACTGCATCAGGAACTGATTGGATAAGAATC yes 509 hsa-miR-218-1-prec miR-218-1 GTTGTGCTTGATCTAACCATGTGGTTGCGAGGTATGAGTA yes 510 hsa-miR-218-2-prec-#1 miR-218-2 TGGTGGAACGATGGAAACGGAACATGGTTCTGTCAAGCAC no 511 hsa-miR-218-2-prec-#2 miR-218-2 TCGCTGCGGGGCTTTCCTTTGTGCTTGATCTAACCATGTG yes 512 hsa-miR-219-prec miR-219 ATTGTCCAAACGCAATTCTCGAGTCTATGGCTCCGGCCGA yes 513 hsa-miR-220-prec miR-220 TGTGGCATTGTAGGGCTCCACACCGTATCTGACACTTTGG yes 514 hsa-miR-221-prec miR-221 CAACAGCTACATTGTCTGCTGGGTTTCAGGCTACCTGGAA yes idem mmu- 515 miR-221- prec-#1 hsa-miR-222-prec-#1 miR-222 CTTTCGTAATCAGCAGCTACATCTGGCTACTGGGTCTCTG yes 516 hsa-miR-222-prec-#2 miR-222 GCTGCTGGAAGGTGTAGGTACCCTCAATGGCTCAGTAGCC no 517 hsa-miR-223-prec miR-223 GAGTGTCAGTTTGTCAAATACCCCAAGTGCGGCACATGCT yes 518 hsa-miR-224-prec miR-224 GGCTTTCAAGTCACTAGTGGTTCCGTTTAGTAGATGATTG yes 519 HSHELA01 — GGCCGCAGCAACCTCGGTTCGTATCCGAGTCACGGCACCA — 520 HSTRNL — TCCGGATGGAGCGTGGGTTCGAATCCCACTTCTGACACCA — 521 HUMTRAB — ATGGTAGAGCGCTCGCTTTGCTTGCGAGAGGTAGCGGGAT — 522 HUMTRF — GATCTAAAGGTCCCTGGTTCGATCCCGGGTTTCGGCACCA — 523 HUMTRMI-#1 — AGCAGAGTGGCGCAGCGGAAGCGTGCTGGGCCCATAACCC — idem 524 MUSTRMI-#1 HUMTRMI-#2 — AACCCAGAGGTCGATGGATCGAAACCATCCTCTGCTACCA — 525 HUMTRN — CAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGT — 526 HUMTRS — TCTAGCGACAGAGTGGTTCAATTCCACCTTTCGGGCGCCA — 527 HUMTRV1A — ACGCGAAAGGTCCCCGGTTCGAAACCGGGCGGAAACACCA — 528 mmu-let-7g-prec mmu-let-7g CTGAGGTAGTAGTTTGTACAGTTTGAGGGTCTATGATACC yes 529 mmu-let-7i-prec mmu-let-7i GCTGAGGTAGTAGTTTGTGCTGTTGGTCGGGTTGTGACAT yes idem hsa- 530 let-7d-v2- prec-#2 mmu-miR-001b-prec mmu-miR-001b ATTCAGTGCTATGGAATGTAAAGAAGTATGTATTTTGGGT yes 531 mmu-miR-001d-prec mmu-miR-001d CTGCTAAGCTATGGAATGTAAAGAAGTATGTATTTCAGGC yes 532 mmu-miR-009-prec-#1 mmu-miR-009 ATCTTTGGTTATCTAGCTGTATGAGTGTATTGGTCTTCAT yes 533 mmu-miR-009-prec-#2 mmu-miR-009- GAGTGTATTGGTCTTCATAAAGCTAGATAACCGAAAGTAA yes idem hsa- 534 miR- 009-2-#2 mmu-miR-010b-prec mmu-miR-010b TACCCTGTAGAACCGAATTTGTGTGGTACCCACATAGTCA yes 535 mmu-miR-023b-prec mmu-miR-023b TTGAGATTAAAATCACATTGCCAGGGATTACCACGCAACC yes 536 mmu-miR-027b-prec mmu-miR-027b TTGGTTTCCGCTTTGTTCACAGTGGCTAAGTTCTGCACCT yes 537 mmu-miR-029b-prec mmu-miR-029b TAAATAGTGATTGTCTAGCACCATTTGAAATCAGTGTTCT yes 538 mmu-miR-030b-prec mmu-miR-030b TGTAAACATCCTACACTCAGCTGTCATACATGCGTTGGCT yes 539 mmu-miR-030e-prec mmu-miR-030e TGTAAACATCCTTGACTGGAAGCTGTAAGGTGTTGAGAGG yes 540 mmu-miR-099a-prec mmu-miR-099a CATAAACCCGTAGATCCGATCTTGTGGTGAAGTGGACCGC yes 541 mmu-miR-099b-prec-#1 mmu-miR-099b GCCTTCGCCGCACACAAGCTCGTGTCTGTGGGTCCGTGTC no idem hsa- 542 miR-099b- prec-19-#1 mmu-miR-099b-prec-#2 mmu-miR-099b CACCCGTAGAACCGACCTTGCGGGGCCTTCGCCGCACACA yes idem hsa- 543 miR-099b- prec-19-#2 mmu-miR-100-prec mmu-miR-100 TGCCACAAACCCGTAGATCCGAACTTGTGCTGATTCTGCA yes 544 mmu-miR-101-prec mmu-miR-101 GCTGTCCATTCTAAAGGTACAGTACTGTGATAACTGAAGG yes 545 mmu-miR-122a-prec-#1 mmu-miR-122a GTGTCCAAACCATCAAACGCCATTATCACACTAAATAGCT no 546 mmu-miR-122a-prec-#2 mmu-miR-122a GCTGTGGAGTGTGACAATGGTGTTTGTGTCCAAACCATCA yes 547 mmu-miR-123-prec-#1 mmu-miR-123 CATTATTACTTTTGGTACGCGCTGTGACACTTCAAACTCG yes 548 mmu-miR-123-prec-#2 mmu-miR-123 GACACTTCAAACTCGTACCGTGAGTAATAATGCGCGGTCA yes 549 mmu-miR-124a-prec mmu-miR-124a TAATGTCTATACAATTAAGGCACGCGGTGAATGCCAAGAG yes 550 mmu-miR-125a-prec mmu-miR-125a TCCCTGAGACCCTTTAACCTGTGAGGACGTCCAGGGTCAC yes 551 mmu-miR-125b-prec-#1 mmu-miR-125b GCCTAGTCCCTGAGACCCTAACTTGTGAGGTATTTTAGTA yes 552 mmu-miR-125b-prec-#2 mmu-miR-125b ATTTTAGTAACATCACAAGTCAGGTTCTTGGGACCTAGGC no 553 mmu-miR-127-prec mmu-miR-127 TTCAGAAAGATCATCGGATCCGTCTGAGCTTGGCTGGTCG yes 554 mmu-miR-128-prec-#1 mmu-miR-128 AGGTTTACATTTCTCACAGTGAACCGGTCTCTTTTTCAGC yes 555 mmu-miR-128-prec-#2 mmu-miR-128 TTGGATTCGGGGCCGTAGCACTGTCTGAGAGGTTTACATT no idem hsa- 556 miR-128a- prec-#1 mmu-miR-129b-prec mmu-miR-129b CTTTTTGCGGTCTGGGCTTGCTGTACATAACTCAATAGCC yes 557 mmu-miR-129-prec mmu-miR-129 CTTTTTGCGGTCTGGGCTTGCTGTTTTCTCGACAGTAGTC yes 558 mmu-miR-130-prec mmu-miR-130 GTCTAACGTGTACCGAGCAGTGCAATGTTAAAAGGGCATC yes 559 mmu-miR-131-3-prec mmu-miR-131-3 AGTGGTGTGGAGTCTTCATAAAGCTAGATAACCGAAAGTA yes 560 mmu-miR-132-prec mmu-miR-132 TGTGGGAACCGGAGGTAACAGTCTACAGCCATGGTCGCCC yes 561 mmu-miR-133-prec mmu-miR-133 ATCGCCTCTTCAATGGATTTGGTCCCCTTCAACCAGCTGT yes 562 mmu-miR-134-prec-#1 mmu-miR-134 GCACTCTGTTCACCCTGTGGGCCACCTAGTCACCAACCCT no 563 mmu-miR-134-prec-#2 mmu-miR-134 TGTGTGACTGGTTGACCAGAGGGGCGTGCACTCTGTTCAC yes 564 mmu-miR-135-prec mmu-miR-135 CTATGGCTTTTTATTCCTATGTGATTCTATTGCTCGCTCA yes 565 mmu-miR-136-prec mmu-miR-136 GAGGACTCCATTTGTTTTGATGATGGATTCTTAAGCTCCA yes 566 mmu-miR-137-prec mmu-miR-137 GGATTACGTTGTTATTGCTTAAGAATACGCGTAGTCGAGG yes idem hsa- 567 miR- 137-prec mmu-miR-138-prec mmu-miR-138 AGCTGGTGTTGTGAATCAGGCCGACGAGCAGCGCATCCTC yes idem hsa- 568 miR-138- 2-prec mmu-miR-140s-prec mmu-miR-140s TTACGTCATGCTGTTCTACCACAGGGTAGAACCACGGACA yes 569 mmu-miR-141-prec mmu-miR-141 GAAGTATGAAGCTCCTAACACTGTCTGGTAAAGATGGCCC yes 570 mmu-miR-142-prec mmu-miR-142 CCCATAAAGTAGAAAGCACTACTAACAGCACTGGAGGGTG yes idem hsa- 571 miR- 142-prec mmu-miR-143-prec mmu-miR-143 TGGTCAGTTGGGAGTCTGAGATGAAGCACTGTAGCTCAGG yes 572 mmu-miR-144-prec mmu-miR-144 GTTTGTGATGAGACACTACAGTATAGATGATGTACTAGTC yes 573 mmu-miR-145-prec mmu-miR-145 ACGGTCCAGTTTTCCCAGGAATCCCTTGGATGCTAAGATG yes 574 mmu-miR-146-prec mmu-miR-146 TGAGAACTGAATTCCATGGGTTATATCAATGTCAGACCTG yes 575 mmu-miR-149-prec mmu-miR-149 GCTCTGGCTCCGTGTCTTCACTCCCGTGTTTGTCCGAGGA yes 576 mmu-miR-150-prec mmu-miR-150 TGTCTCCCAACCCTTGTACCAGTGCTGTGCCTCAGACCCT yes 577 mmu-miR-151-prec mmu-miR-151 TATGTCTCCTCCCTACTAGACTGAGGCTCCTTGAGGGACA yes 578 mmu-miR-152-prec mmu-miR-152 ACTCGGGCTCTGGAGCAGTCAGTGCATGACAGAACTTGGG yes idem hsa- 579 miR-152- prec-#1 mmu-miR-153-prec mmu-miR-153 TAATATGAGCCCAGTTGCATAGTGACAAAAGTGATCATTG yes 580 mmu-miR-154-prec mmu-miR-154 AGATAGGTTATCCGTGTTGCCTTCGCTTTATTCGTGACGA yes 581 mmu-miR-155-prec mmu-miR-155 TTAATGCTAATTGTGATAGGGGTTTTGGCCTCTGACTGAC yes 582 mmu-miR-181-prec mmu-miR-181 CCATGGAACATTCAACGCTGTCGGTGAGTTTGGGATTCAA yes 583 mmu-miR-182-prec mmu-miR-182 TTTGGCAATGGTAGAACTCACACCGGTAAGGTAATGGGAC yes 584 mmu-miR-183-prec-#1 mmu-miR-183 AACAGTCTCAGTCAGTGAATTACCGAAGGGCCATAAACAG no 585 mmu-miR-183-prec-#2 mmu-miR-183 TATGGCACTGGTAGAATTCACTGTGAACAGTCTCAGTCAG yes 586 mmu-miR-184-prec mmu-miR-184 TGTGACTCTAAGTGTTGGACGGAGAACTGATAAGGGTAGG yes 587 mmu-miR-185-prec mmu-miR-185 GGGATTGGAGAGAAAGGCAGTTCCTGATGGTCCCCTCCCA yes 588 mmu-miR-186-prec mmu-miR-186 CAAAGAATTCTCCTTTTGGGCTTTCTCATTTTATTTTAAG yes 589 mmu-miR-187-prec mmu-miR-187 GGGCGCTGCTCTGACCCCTCGTGTCTTGTGTTGCAGCCGG yes 590 mmu-miR-188-prec mmu-miR-188 TCACATCCCTTGCATGGTGGAGGGTGAGCTCTCTGAAAAC yes 591 mmu-miR-189-prec mmu-miR-189 CGGTGCCTACTGAGCTGATATCAGTTCTCATTTCACACAC yes 592 mmu-miR-190-prec mmu-miR-190 CTGTGTGATATGTTTGATATATTAGGTTGTTATTTAATCC yes 593 mmu-miR-191-prec mmu-miR-191 CAACGGAATCCCAAAAGCAGCTGTTGTCTCCAGAGCATTC yes idem hsa- 594 miR- 191-prec mmu-miR-192-2/3-prec mmu-miR-192-2/3 CTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTC yes 595 mmu-miR-193-prec mmu-miR-193 TGAGAGTGTCAGTTCAACTGGCCTACAAAGTCCCAGTCCT yes 596 mmu-miR-194-prec mmu-miR-194 ATCGGGTGTAACAGCAACTCCATGTGGACTGTGCTCGGAT yes 597 mmu-miR-195-prec mmu-miR-195 TAGCAGCACAGAAATATTGGCATGGGGAAGTGAGTCTGCC yes 598 mmu-miR-196-prec mmu-miR-196 GTAGGTAGTTTCATGTTGTTGGGCCTGGCTTTCTGAACAC yes 599 mmu-miR-199as-prec mmu-miR-199as GAGGCTGGGACATGTACAGTAGTCTGCACATTGGTTAGGC yes 600 mmu-miR-200a-prec-#1 mmu-miR-200a TAGTGTCTGATCTCTAATACTGCCTGGTAATGATGACGGC yes 601 mmu-miR-200a-prec-#2 mmu-miR-200a CCGTGGCCATCTTACTGGGCAGCATTGGATAGTGTCTGAT no 602 mmu-miR-201-prec mmu-miR-201 TACCTTACTCAGTAAGGCATTGTTCTTCTATATTAATAAA yes 603 mmu-miR-202-prec mmu-miR-202 GATCTGGTCTAAAGAGGTATAGCGCATGGGAAGATGGAGC yes 604 mmu-miR-203-prec-#1 mmu-miR-203 GGTCCAGTGGTTCTTGACAGTTCAACAGTTCTGTAGCACA no 605 mmu-miR-203-prec-#2 mmu-miR-203 GTAGCACAATTGTGAAATGTTTAGGACCACTAGACCCGGC yes 606 mmu-miR-204-prec mmu-miR-204 TTCCCTTTGTCATCCTATGCCTGAGAATATATGAAGGAGG yes 607 mmu-miR-205-prec mmu-miR-205 GTCCTTCATTCCACCGGAGTCTGTCTTATGCCAACCAGAT yes 608 mmu-miR-206-prec mmu-miR-206 TAGATATCTCAGCACTATGGAATGTAAGGAAGTGTGTGGT yes 609 mmu-miR-207-prec mmu-miR-207 GCTGCGGCTTGCGCTTCTCCTGGCTCTCCTCCCTCTCCTT yes 610 mmu-miR-212-prec-#1 mmu-miR-212 CTTCAGTAACAGTCTCCAGTCACGGCCACCGACGCCTGGC yes 611 mmu-miR-212-prec-#2 mmu-miR-212 AGCGCGCCGGCACCTTGGCTCTAGACTGCTTACTGCCCGG no 612 mmu-miR-213-prec mmu-miR-213 AACATTCATTGCTGTCGGTGGGTTGAACTGTGTGGACAAG yes idem hsa- 613 miR-213- prec-#1 mmu-miR-214-prec mmu-miR-214 TGTACAGCAGGCACAGACAGGCAGTCACATGACAACCCAG yes idem hsa- 614 miR- 214-prec mmu-miR-215-prec mmu-miR-215 CAGGAGAATGACCTATGATTTGACAGACCGTGCAGCTGTG yes 615 mmu-miR-216-prec-#1 mmu-miR-216 GAGATGTCCCTATCATTCCTCACAGTGGTCTCTGGGATTA no 616 mmu-miR-216-prec-#2 mmu-miR-216 ATGGCTATGAGTTGGTTTAATCTCAGCTGGCAACTGTGAG yes 617 mmu-miR-217-prec-#1 mmu-miR-217 GCAGATACTGCATCAGGAACTGACTGGATAAGACTTAATC yes 618 mmu-miR-217-prec-#2 mmu-miR-217 CCCCATCAGTTCCTAATGCATTGCCTTCAGCATCTAAACA no 619 mmu-miR-218-2-prec-#1 mmu-miR-218-2 GGGCTTTCCTTTGTGCTTGATCTAACCATGTGGTGGAACG yes 620 mmu-miR-218-2-prec-#2 mmu-miR-218-2 GTGGTGGAACGATGGAAACGGAACATGGTTCTGTCAAGCA no 621 mmu-miR-219-prec-#1 mmu-miR-219 TCCTGATTGTCCAAACGCAATTCTCGAGTCTCTGGCTCCG yes 622 mmu-miR-219-prec-#2 mmu-miR-219 CTCTGGCTCCGGCCGAGAGTTGCGTCTGGACGTCCCGAGC no 623 mmu-miR-221-prec-#1 mmu-miR-221 CAACAGCTACATTGTCTGCTGGGTTTCAGGCTACCTGGAA yes idem hsa- 624 miR- 221-prec mmu-miR-221-prec-#2 mmu-miR-221 GGCATACAATGTAGATTTCTGTGTTTGTTAGGCAACAGCT no 625 mmu-miR-222-prec mmu-miR-222 TTGGTAATCAGCAGCTACATCTGGCTACTGGGTCTCTGGT yes 626 mmu-miR-223-prec mmu-miR-223 AGAGTGTCAGTTTGTCAAATACCCCAAGTGTGGCTCATGC yes 627 mmu-miR-224- mmu-miR-224- TAAGTCACTAGTGGTTCCGTTTAGTAGATGGTCTGTGCAT yes 628 precformer175-#1 (miR-175) mmu-miR-224- mmu-miR-224- TGCATTGTTTCAAAATGGTGCCCTAGTGACTACAAAGCCC no 629 precformer175-#2 (miR-175) MUSTRF — TAGACTGAAGATCTAAAGGTCCCTGGTTCGATCCCGGGTT — 630 MUSTRM4 — AATCTGAAGGTCGTGAGTTCGATCCTCACACGGGGCACCA — 631 MUSTRMI-#1 — AGCAGAGTGGCGCAGCGGAAGCGTGCTGGGCCCATAACCC — idem 632 HUMTRMI-#1 MUSTRMI-#2 — CCCATAACCCAGAGGTCGATGGATCGAAACCATCCTCTGC — 633 MUSTRNAH — TGCGTTGTGGCCGCAGCAACCTCGGTTCGAATCCGAGTCA — 634 MUSTRP2 — GCTCGTTGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGA — 635 MUSTRS — AGCTGTTTAGCGACAGAGTGGTTCAATTCCACCTTTCGGG — 636 MUSTRV1MN — TTCCGTAGTGTAGTGGTTATCACGCTCGCCTGACACGCGA — 637 Oligonucleotide primer — 5′ biotin-AAA-AAA-AAA-AAA-(biotin)AAA-AAA- — 638 #1 AAA-AAA-NNN-NNN-NN 3′ Oligonucleotide primer — 5′ biotin-(biotin)-AAA-NNN-NNN-NN 3′ — 639 #2 Oligonucleotide primer — 5′ GCC-AGT-GAA-TTG-TAA-TAC-GAC-TCA-CTA-TAG- — 640 #3 GGA-GGC-GGN-NNN-NNN-N 3′

miRNA Microarray Fabrication. 40-mer 5′ amine modified C6 oligonucleotides were resuspended in 50 mM phosphate buffer pH 8.0 at 20 mM concentration. The individual oligonucleotide-probe was printed in triplicate on Amersham CodeLink™ activated slides under 45% humidity by GeneMachine OmniGrid™ 100 Microarrayer in 2×2 pin configuration and 20×20 spot configuration of each subarray. The spot diameter was 100 μm and distance from center to center was 200 μm. The printed miRNA microarrays were further chemically covalently-coupled under 70% humidity overnight. The miRNA microarrays were ready for sample hybridization after additional blocking and washing steps.

Target Preparation. Five μg of total RNA were separately added to a reaction mix in a final volume of 12 μA, containing 1 μg of [3′(N)8-(A)12-biotin-(A)12-biotin 5′] oligonucleotide primer. The mixture was incubated for 10 min at 70° C. and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl 0.1 M DTT, 1 μl of 10 mM dNTP mix and 1 μl Superscript™ II RNaseH⁻ reverse transcriptase (200 U/μl) was added to a final volume of 20 μA, and the mixture incubated for 90 min in a 37° C. water bath. After incubation for first strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first strand reaction mix and incubated at 65° C. for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then 5 μl of 1 M Tris-HCl, pH 7.6 (Sigma) was added to neutralize the reaction mix and labeled targets were stored in 28.5 μl at −80° C. until chip hybridization.

Array Hybridization. Labeled targets from 5 μg of total RNA were used for hybridization on each KCC/TJU miRNA microarray containing 368 probes in triplicate, corresponding to 245 human and mouse miRNA genes. All probes on these microarrays were 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6×SSPE/30% formamide at 25° C. for 18 hours, washed in 0.75×TNT at 37° C. for 40 min, and processed using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate. Processed slides were scanned using a Perkin Elmer ScanArray® XL5K Scanner with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 microns.

Data Analysis. Images were quantified by QuantArray® Software (PerkinElmer). Signal intensities for each spot were calculated by subtracting local background (based on the median intensity of the area surrounding each spot) from total intensities. Raw data were normalized and analyzed using the GeneSpring® software version 6.1.1 (Silicon Genetics, Redwood City, Calif.). GeneSpring generates an average value of the three spot replicates of each miRNA. Following data transformation (to convert any negative value to 0.01), normalization was performed by using a per-chip 50th percentile method that normalizes each chip on its median allowing comparison among chips. Hierarchical clustering for both genes and conditions were then generated by using standard correlation as a measure of similarity. To highlight genes that characterize each tissue, a per-gene on median normalization was performed, which normalizes the expression of every miRNA on its median among samples.

Samples. HeLa cells were purchased from ATCC and grown as recommended. Mouse macrophage cell line RAW264.7 (established from BALB/c mice) was also used (Dumitru, C. D., Ceci, J. D., Tsatsanis, C., Kontoyiannis, D., Stamatakis, K., Lin, J. H., Patriotis, C., Jenkins, N. A., Copeland, N. G., Kollias, G. & Tsichlis, P. N. (2000) Cell 103, 1071-83). RNA from 20 normal human tissues, including 18 of adult origin (7 hematopoietic: bone marrow, lymphocytes B, T, and CD5+ cells from 2 individuals, peripheral blood leukocytes derived from three healthy donors, spleen, and thymus; and 11 solid tissues, including brain, breast, ovary, testis, prostate, lung, heart, kidney, liver, skeletal muscle, and placenta) and 2 of fetal origin (fetal liver and fetal brain) were assessed for miRNA expression. Each RNA was labeled and hybridized in duplicate and the average expression was calculated. For all the normal tissues, except lymphocytes B, T and CD5+ cells, total RNA was purchased from Ambion (Austin, Tex.).

Cell Preparation. Mononuclear cells (MNC) from peripheral blood of normal donors were separated by Ficoll-Hypaque density gradients. T cells were purified from these MNC by rosetting with neuraminidase treated SRBC and depletion of contaminant monocytes (Cd11b+), natural killer cells (CD16+) and B lymphocytes (CD19+) were purified using magnetic beads (Dynabeads, Unipath, Milano, Italy) and specific monoclonal antibodies (Becton Dickinson, San Jose, Calif.). Total B cells and CD5+ B cells were prepared from tonsils as described (Dono, M., Zupo, S., Leanza, N., Melioli, G., Fogli, M., Melagrana, A., Chiorazzi, N. & Ferrarini, M. (2000) J. Immunol. 164, 5596-604). Briefly, tonsils were obtained from patients in the pediatric age group undergoing routine tonsillectomies, after informed consent. Purified B cells were prepared by rosetting T cells from MNC cells with neuraminidase treated SRBC. In order to obtain CD5+ B cells, purified B cells were incubated with anti CD5 monoclonal antibody followed by goat anti mouse Ig conjugated with magnetic microbeads. CD5+ B cells were positively selected by collecting the cells retained on the magnetic column MS by Mini MACS system (Miltenyi Biotec, Auburn, Calif.). The degree of purification of the cell preparations was higher than 95%, as assessed by flow cytometry.

RNA Extraction and Northern Blots. Total RNA isolation and blots were performed as described (Calin, et al., (2002) Proc Natl Acad Sc USA. 99, 15524-15529). After RNA isolation, the washing step with ethanol was not performed, or if performed, the tube walls were rinsed with 75% ethanol without perturbing the RNA pellet (Lagos-Quintana, et al., (2001) Science 294, 853-858). For reuse, blots were stripped by boiling in 0.1% aqueous SDS/0.1×SSC for 10 min, and were reprobed. 5S rRNA stained with ethidium bromide served as a loading control.

Quantitative RT-PCR for miRNA Precursors. Quantitative RT-PCR was performed as described (Schmittgen, T. D., Jiang, J., Liu, Q. & Yang, L. (2004) Nucleic Acid Research 32, 43-53). Briefly, RNA was reverse transcribed to cDNA with gene-specific primers and Thermoscript, and the relative amount of each miRNA to both U6 RNA and tRNA for initiator methionine was described using the equation 2^(−dc)T, where dC_(T)=(C_(TmiRNA)−C_(TU6 or HUMTMI RNA)). The miRNAs analyzed included miR-15a, miR-16-1, miR-18, miR-20, miR-21, miR-28-2, miR-30d, miR-93-1, miR-105, miR-124a-2, miR-147, miR-216, miR-219, and miR-224. The primers used were as published (Schmittgen, T. D., Jiang, J., Liu, Q. & Yang, L. (2004) Nucleic Acid Research 32, 43-53).

Microarray Data Submission. All data were submitted using MIAMExpress to Array Express database and each of the 44 samples described here received an ID number ranging from SAMPLE169150SUB621 to SAMPLE 169193SIUB621.

Results

Hybridization Sensitivity. The hybridization sensitivity of the miRNA microarray was tested using various quantities of total RNA from HeLa cells, starting from 2.5 μg up to 20 μg. The coefficients of correlation between the 5 μg experiment versus the 2.5, 10 and 20 μg experiments, were 0.98, 0.99 and 0.97 respectively. These results clearly show high inter-assay reproducibility, even in the presence of large differences in RNA quantities. In addition, standard deviation calculated for miRNA triplicates was below 10% for the vast majority (>95%) of oligonucleotides. All other experiments described here were performed with 5 μg of total RNA.

Microarray specificity. To test the specificity of the microchip, miRNA expression in human blood leukocytes from three healthy donors and 2 samples of mouse macrophages was analyzed. Samples derived from the same type of tissue presented homogenous patterns of miRNA expression. Furthermore, the pattern of hybridization is different for the two species. To confirm microarray results, the same RNA samples from mouse macrophages and HeLa cells were also analyzed by quantitative RT-PCR for a randomly selected set of 14 miRNAs (Schmittgen, T. D., Jiang, J., Liu, Q. & Yang, L. (2004) Nucleic Acid Research 32, 43-53). When we were able to amplify a miRNA precursor for which a correspondent oligonucleotide was present on the chip (hsa-miR-15a, hsa-mir-30d, mmu-miR-219 and mmu-miR-224) the concordance between the two techniques was 100%. Furthermore, it has been reported that expression levels of the active miRNA and the precursor pre-miRNA are different in the same sample (Calin, et al. (2002) Proc Natl Acad Sc USA. 99, 15524-15529; Mourelatos, et al. (2002) Genes Dev 16, 720-728; Lagos-Quintana, et al. (2002) Curr Biol 12, 735-739); in fact, for another 10 miRNAs for which only the oligonucleotide corresponding to the active version was present on the chip, no concordance with quantitative real-time PCR results was observed for the precursor.

The stringency of hybridization was, in several instances, sufficient to distinguish nucleotide mismatches for members of closely related miRNA families and very similar sequences gave distinct expression profiles (for example let-7a-1 and let-7f-2 which are 89% similar in an 88 nucleotide sequence). Therefore, each quantified result represents the specific expression of a single miRNA member and not the combined expression of the entire family. In other cases, when a portion of oligonucleotide was 100% identical for two probes (for example, the 23 mer of active molecule present in the 40-mer oligonucleotides for both mir-16 sequences from chromosome 13 and chromosome 3), very similar profiles were observed. Therefore, both sequence similarity and secondary structure influence the cross-hybridization between different molecules on this type of microarray.

miRNA Expression in Normal Human Tissues. To further validate reliability of the microarray, we analyzed a panel of 20 RNAs from human normal tissues, including 18 of adult origin (7 hematopoietic and 11 solid tissues) and 2 of fetal origin (fetal liver and brain). For 15 of them, at least two different RNA samples or two replicates from the same preparation were used (for a detailed list of samples see the above Methods). The results demonstrated that different tissues have distinctive patterns of miRNome expression (defined as the full complement of miRNAs in a cell) with each tissue presenting a specific signature. Using unsupervised hierarchical clustering, the same types of tissue from different individuals clustered together. The hematopoietic tissues presented two distinct clusters, the first one containing CD5+ cells, T lymphocytes, and leukocytes and the second cluster containing bone marrow, fetal liver and B lymphocytes. Of note, RNA of fetal or adult type from the same tissue origin (brain) present different miRNA expression pattern. The results demonstrated that some miRNAs are highly expressed in only one or few tissues, such as miR-1b-2 or miR-99b in brain, and the closely related members miR-133a and miR-133b in skeletal muscle, heart and prostate. The types of normalization of the GeneSpring software (on 50% with or without a per-gene on median normalization) did not influence these results.

To verify these data, Northern blot analysis was performed on total RNA used in the microarray experiments, using four miRNA probes: miR-16-1, miR-26a, miR-99a and miR-223. In each case, the concordance between the two techniques was high: in all instances the highest and the lowest expression levels were concordant. For example high levels of miR-223 expression were found by both techniques in spleen, for miR-16-1 in CD5+ cells, while very low levels were found in brain for both miRNAs. Moreover, in several instances (for example miR-15a), we were able to identify the same pattern of expression for the precursor and the active miR with both microchip and Northern blots.

We also compared the published expression data for cloned human and mouse miRNAs by Northern blot analyses against the microarray results. We found that the concordance with the chip data is high for both pattern and intensity of expression. For example, miR-133 was reported to be strongly expressed only in the skeletal muscle and heart (Sempere, et al. (2003) Genome Biol. 5, R13), precisely as was found with the microarray, while miR-125 and mir-128 were reported to be highly expressed in brain (Sempere, et al. (2003) Genome Biol. 5, R13), a finding confirmed on the microchip.

Example 11 miRNA Profiling of B-Cell Chronic Lymphocytic Leukemia Samples Introduction

The miRNome expression in 38 individual human B-cell chronic lymphocytic leukemia (CLL) cell samples was determined utilizing the microchip of Example 10. One normal lymph node sample and 5 samples from healthy donors, including two tonsillar CD5+ B lymphocyte samples and three blood mononuclear cell (MNC) samples, were included for comparison. As hereinafter demonstrated, two distinct clusters of CLL samples associated with the presence or the absence of Zap-70 expression, a predictor of early disease progression. Two miRNA signatures were associated with presence or absence of mutations in the expressed immunoglobulin variable-region genes or with deletions at 13q14 respectively.

Materials and Methods

The following methods were employed in the miRNome expression study.

Tissue Samples and CLL Samples. 47 samples were used for this study, including 41 samples from 38 patients with CLL, and 6 normal samples, including one lymph node, tonsillar CD5+ B cells from two normal donors and blood mononuclear cells from three normal donors. For three cases, two independent samples were collected and processed. CLL samples were obtained after informed consent from patients diagnosed with CLL at the CLL Research Consortium institutions. Briefly, blood was obtained from CLL patients, mononuclear cells were isolated through Ficoll/Hypaque gradient centrifugation (Amersham Pharmacia Biotech) and processed for RNA extraction according to described protocols (M. Lagos-Quintana, R. Rauhut, W. Lendeckel, T. Tuschl, Science 294, 853-858 (2001)). For the majority of samples clinical and biological information, such as age at diagnosis, sex, Rai stage, presence/absence of treatment, ZAP-70 expression, IgV_(H) gene mutation status were available, as provided in Table 9:

TABLE 9 Clinical and biological data for the patients in the two CLL clusters* Semnification Dx Age Sex % Zap VH gene Mut CLL cluster 1 50.68 F 30.4 VH4-04 Neg CLL cluster 1 57.4 F 50.6 VH3-33 Pos CLL cluster 1 67.49 M 0.5 VH3-23 Pos CLL cluster 1 59.74 M 31.5 VH3-09 Pos CLL cluster 1 77.49 F 0.3 VH5-51 Pos CLL cluster 1 58.19 F 3.6 VH3-30/3-30.5 Pos CLL cluster 1 43 M 41.9 VH4-30.1/4-31 Neg CLL cluster 1 61.82 M 83.2 VH1-03 Neg CLL cluster 1 48.44 F 69.3 VH1-69 Neg CLL cluster 2 72.59 M 2.2 VH3-72 Pos CLL cluster 2 45.19 M 7.3 VH1-69 Pos CLL cluster 2 56.39 F 0.6 VH3-15 Pos CLL cluster 2 61.85 F 0.1 VH3-30 Neg CLL cluster 2 60.89 F 0.1 VH2-05 Pos CLL cluster 2 62.66 M 1 VH3-07 Pos CLL cluster 2 49.85 M 3.6 VH3-74 Pos CLL cluster 2 70.62 M 0.2 VH3-13 Pos CLL cluster 2 68.02 F 0.9 VH3-30.3 Pos CLL cluster 2 46.84 M 62.2 VH3-30/3-30.5 Neg CLL cluster 2 51.31 F 91.9 VH4-59 Neg CLL cluster 2 52.6 F 10.6 VH3-07 Pos CLL cluster 2 56.04 F 0.4 VH3-72 Pos CLL cluster 2 61.67 M 77.9 VH3-74 Neg CLL cluster 2 62.14 F 46 VH1-02 Pos CLL cluster 2 39.29 F 10.1 VH3-07 Neg *data for ZAP-70 expression were available for 25 patients (25/38, 66%).

Cell Preparation. Mononuclear cells (MNC) from peripheral blood of normal donors were separated by Ficoll-Hypaque density gradients. T cells were purified from these MNC by rosetting with neuraminidase-treated sheep red blood cells (SRBC) and depletion of contaminant monocytes (Cd11b+), natural killer cells (CD16+) and B lymphocytes (CD19+) were purified using magnetic beads (Dynabeads, Unipath, Milano, Italy) and specific monoclonal antibodies (Becton Dickinson, San Jose, Calif.). Total B cells and CD5+ B cells were prepared from tonsillar lymphocytes as described (M. Dono et al., J. Immunol. 164, 5596-604. (2000)). Briefly, tonsils were obtained from patients in the pediatric age group undergoing routine tonsillectomies, after informed consent. Purified B cells were prepared by rosetting T cells from MNC cells with neuraminidase treated SRBC. In order to obtain CD5+ B cells, purified B cells were incubated with anti CD5 monoclonal antibody followed by goat anti mouse Ig conjugated with magnetic microbeads. CD5+ B cells were positively selected by collecting the cells retained on the magnetic column MS by Mini MACS system (Miltenyi Biotec, Auburn, Calif.). The degree of purification of the cell preparations was higher than 95%, as assessed by flow cytometry.

RNA Extraction and Northern Blots. Total RNA isolation and blots were performed as described (G. A. Calin et al., Proc Natl Acad Sc USA. 99, 15524-15529 (2002)). After RNA isolation, the washing step with ethanol was not performed, or if performed, the tube walls were rinsed with 75% ethanol without perturbing the RNA pellet (M. Lagos-Quintana, R. Rauhut, W. Lendeckel, T. Tuschl, Science 294, 853-858 (2001)). For reuse, blots were stripped by boiling in 0.1% aqueous SDS/0.1×SSC for 10 minutes, and were reprobed. 5S rRNA stained with ethidium bromide served as a sample loading control.

Microarray Experiments. RNA blot analysis was performed as described in Example 10, utilizing the microchip of Example 10. Briefly, labeled targets from 5 μg of total RNA was used for hybridization on each miRNA microarray chip containing 368 probes in triplicate, corresponding to 245 human and mouse miRNA genes. The microarrays were hybridized in 6×SSPE/30% formamide at 25° C. for 18 hrs, washed in 0.75×TNT at 37° C. for 40 min, and processed using a method of direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate. Processed slides were scanned using a Perkin Elmer ScanArray® XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 microns.

Data Analysis. Expression profiles were analyzed in duplicate independent experiments starting from the same cell sample. Raw data were normalized and analyzed in GeneSpring® software version 6.1.1 (Silicon Genetics, Redwood City, Calif.). GeneSpring generated an average value of the three spot replicates of each miRNA. Following data transformation (to convert any negative value to 0.01), normalization was performed by using a per-chip on median normalization method and a normalization to specific samples, expressly to the two CD5+ B cell samples, used as common reference for miRNA expression. Hierarchical clustering for both genes and conditions were generated by using standard correlation as a measure of similarity. To identify genes with statistically significant differences between sample groups (i.e. CLL cells and CD5+ B cells, CLL and MNC, CLL samples with or without IgV_(H) mutations or CLL cases with or without 13q14.3 deletion), a Welch's approximate t-test for two groups (variances not assumed equal) with a p-value cutoff of 0.05 and Benjamini and Hochberg False Discovery Rate as multiple testing correction were performed.

Real Time PCR. Quantitative real-time PCR was performed as described by T. D. Schmittgen, J. Jiang, Q. Liu, L. Yang, Nucleic Acid Research 32, 43-53 (2004). Briefly, RNA was reverse transcribed to cDNA with gene-specific primers and Thermoscript and the relative amount of each miRNA to tRNA for initiator methionine was described, using the equation 2^(−dc)T, where dC_(T)=(C_(TmiRNA)−C_(TU6 or HUMTMI RNA)). The set of analyzed miRNAs included miR-15a, miR-16-1, miR-18, miR-20, and miR-21. The primers used were as published (Id.).

Western Blotting. Protein lysates were prepared from the leukemia cells of 7 CLL patients and from isolated tonsillar CD5⁺ B cells. Western blot analysis was performed with a polyclonal Pten antibody (Cell Signaling Technology, Beverly, Mass.) and was normalized using an anti-actin antibody (Sigma, St. Louis, Mo.).

Microarray Data Submission. All data were submitted using MIAMExpress to the Array Express database and each of the 39 CLL samples described here received an ID number ranging from SAMPLE 169194SUB621 to SAMPLE 169234SIUB621.

Results

Comparison of miRNA expression in CLL cells vs. normal CD5+ B cells and normal blood mononuclear cells. Normal CD5+ B cells utilized in this study are considered as normal cell counterparts to CLL B cells. As described in Table 10, two groups of differentially expressed miRNAs, the first composed of 55 genes and the second of 29 genes, had statistically significant differences in expression levels between the various groups (p<0.05 using Welch t-test as described in Materials and Methods, above). Only 6 miRNA are shared between the two lists, confirming the results of Example 10 showing distinct miRNome signatures in CD5⁺ B cells and leukocytes. When both pre-miRNA and mature miRNA were observed to be dysregulated (such as for miR-123, miR-132 or miR-136), the same type of variation in CLL samples with respect to CD5 or MNC was noted in every case. Also, for some miRNA genomic clusters all members were aberrantly regulated (such as the up-regulated 7q32 group encompassing miR-96-miR182-miR183), while for others only some members were abnormally expressed (such as the 13q31 genomic cluster where two out of six members, miR-19 and miR-92-1, were strongly up-regulated and two, miR-17 and miR-20, were moderately down-regulated). Without wishing to be bound by any theory, the results illustrate the complexity of the patterns of miRNA expression in CLL and indicate the existence of mechanisms regulating individual miRNA genes that map in the same chromosome region. In confirmation of the accuracy of the data, miR-223, reported to be expressed at high levels in granulocytes (M. Lagos-Quintana et al., Curr Biol 12, 735-739 (2002)), was expressed at significantly lower levels in the CLL samples than in the MNC, but at about the same level as that noted for CD5⁺ B cells (which generally constitute less than a few percent of blood MNC).

TABLE 10 Differentially expressed miRNAs in CLLs versus CD5+ cells or CLLs versus MNC (bold)* Oligonucleotide probe microRNA Chr location FRA associated P-value Type hsa-let-7a-2-precNo1 let-7a-2 11q24.1 0.014 Down hsa-let-7d-v2-precNo2 let-7d-v2-prec 12q14.1 4.29E−04 Down hsa-let-7f-1-precNo1 let-7f-1 09q22.2 FRA9D 3.09E−29 Down hsa-mir-009-2No1 miR-9-2 5q14 0.013 up hsa-mir-010a-precNo2 miR-10a-prec 17q21.3 0.007 up hsa-mir-010b-precNo1 mir-10b 02q31 1.10E−15 up hsa-mir-015b-precNo2 mir-15b-prec 03q26.1 5.79E−14 up hsa-mir-017-precNo2 mir-17-prec 13q31 0.042 Down hsa-mir-017-precNo2 mir-17-prec 13q31 0.049 Down hsa-mir-019a-prec mir-19a 13q31 5.16E−17 up hsa-mir-020-prec mir-20a 13q31 0.038 Down hsa-mir-021-prec-17No2 mir-21-prec 17q23.2 FRA17B 0.044 up hsa-mir-022-prec mir-22 17p13.3 7.16E−04 up hsa-mir-023a-prec mir-23a 19p13.2 0.011 Down hsa-mir-024-1-precNo1 mir-24-1 09q22.1 FRA9D 0.002 Down hsa-mir-024-1-precNo2 mir-24-1-prec 09q22.1 FRA9D 7.35E−20 up hsa-mir-024-2-prec mir-24-2 19p13.2 5.69E−17 Down hsa-mir-025-prec mir-25 07q22 FRA7F 9.52E−04 Down hsa-mir-027b-prec mir-27b 09q22.1 FRA9D 0.046 Down hsa-mir-029a-2No1 mir-29a-2 07q32 FRA7H 0.013 up hsa-mir-029a-2No2 mir-29a-2-prec 07q32 FRA7H 0.001 up hsa-mir-029c-prec mir-29c 01q32.2-32.3 0.002 up hsa-mir-030a-precNo1 mir-30a 06q12-13 0.004 Down hsa-mir-030a-precNo2 mir-30a-prec 06q12-13 0.034 Down hsa-mir-030d-precNo2 mir-30d-prec 08q24.2 0.008 Down hsa-mir-033-prec mir-33 22q13.2 1.56E−18 up hsa-mir-034precNo1 mir-34 01p36.22 6.00E−06 up hsa-mir-092-prec-13=092-1No1 mir-92-1 13q31 1.70E−12 up hsa-mir-092-prec-13=092-1No2 mir-92-prec 13q31 0.021 Down hsa-mir-092-prec-X=092-2 mir-92-2 Xq26.2 3.38E−04 Down hsa-mir-092-prec-X=092-2 mir-92-2 Xq26.2 0.042 Down hsa-mir-096-prec-7No1 mir-96 07q32 FRA7H 1.79E−04 up hsa-mir-099-prec-21 mir-99 21q11.2 0.001 Down hsa-mir-101-1/2-precNo1 mir-101 01p31.3 FRA1C 1.26E−08 up hsa-mir-101-1/2-precNo2 mir-101-prec 01p31.3 0.017 up hsa-mir-103-prec-5=103-1 mir-103-1 05q35.1 0.002 Down hsa-mir-103-prec-5=103-1 mir-103-1 05q35.1 0.007 Down hsa-mir-105-prec-X.1=105-1 mir-105-1 Xq28 FRAXF 1.55E−05 up hsa-mir-107-prec-10 mir-107 10q23.31 0.002 Down hsa-mir-123-precNo1 mir-123 09q34 2.80E−16 up hsa-mir-123-precNo1 mir-123 09q34 0.021 Down hsa-mir-123-precNo2 mir-123-prec 09q34 0.021 Down hsa-mir-124a-2-prec mir-124a-2 08q12.2 4.33E−06 up hsa-mir-128b-precNo1 mir-128b 03p22 5.05E−07 Down hsa-mir-128b-precNo2 mir-128-prec 03p22 0.007 up hsa-mir-130a-precNo2 mir-130a-prec 11q12 0.010 Down hsa-mir-130a-precNo2 mir-130a-prec 11q12 0.050 up hsa-mir-132-precNo1 mir-132 11q12 1.68E−07 up hsa-mir-132-precNo2 mir-132-prec 17p13.3 8.62E−04 up hsa-mir-134-precNo1 mir-134 14q32 6.01E−08 up hsa-mir-136-precNo1 mir-136 14q32 0.003 up hsa-mir-136-precNo2 mir-136-prec 14q32 7.44E−04 up hsa-mir-137-prec mir-137 01p21-22 0.013 up hsa-mir-138-1-prec mir-138-1 03p21 2.53E−04 up hsa-mir-140No1 mir-140 16q22.1 2.41E−16 up hsa-mir-141-precNo1 mir-141 12p13 7.91E−08 up hsa-mir-141-precNo2 mir-141-prec 12p13 1.39E−08 up hsa-mir-142-prec mir-142 17q23 FRA17B 0.004 Down hsa-mir-145-prec mir-145 05q32-33 0.021 Down hsa-mir-146-prec mir-146 05q34 1.03E−08 Down hsa-mir-148-prec mir-148 07p15 3.48E−05 up hsa-mir-152-precNo1 mir-152 17q21 0.003 up hsa-mir-152-precNo2 mir-152-prec 17q21 3.35E−05 up hsa-mir-153-1-prec1 mir-153 02q36 0.005 up hsa-mir-153-1-prec2 mir-153-prec 02q36 1.48E−08 up hsa-mir-154-prec1No1 mir-154 14q32 1.14E−10 up hsa-mir-155-prec mir-155 21q21 0.029 up hsa-mir-181b-precNo2 mir-181b-prec 01q31.2-q32.1 3.26E−06 up hsa-mir-181c-precNo2 mir-181c-prec 19p13.3 0.003 up hsa-mir-182-precNo2 mir-182-prec 07q32 FRA7H 0.001 up hsa-mir-183-precNo2 mir-183-prec 07q32 FRA7H 1.26E−23 up hsa-mir-184-precNo1 mir-184 15q24 0.007 up hsa-mir-188-prec mir-188 Xp11.23-p11.2 6.08E−11 up hsa-mir-190-prec mir-190 15q21 FRA15A 1.48E−20 up hsa-mir-191-prec mir-191 03p21 9.14E−05 Down hsa-mir-192-2/3No1 mir-192 11q13 2.00E−07 Down hsa-mir-193-precNo2 mir-193-prec 17q11.2 9.14E−05 up hsa-mir-194-precNo1 mir-194 01q41 FRA1H 0.002 up hsa-mir-196-2-precNo1 mir-196-2 12q13 FRA12A 4.94E−08 up hsa-mir-196-2-precNo2 mir-196-2-prec 12q13 FRA12A 0.040 up hsa-mir-197-prec mir-197 01p13 0.003 Down hsa-mir-200a-prec mir-200a 01p36.3 9.14E−05 up hsa-mir-204-precNo2 mir-204-prec 09q21.1 8.55E−04 up hsa-mir-206-precNo1 mir-206 06p12 0.003 Down hsa-mir-210-prec mir-210 11p15 0.009 Down hsa-mir-212-precNo1 mir-212 17p13.3 0.045 Down hsa-mir-213-precNo1 mir-213 01q31.3-q32.1 1.47E−33 Down hsa-mir-217-precNo2 mir-217 02p16 3.85E−09 up hsa-mir-220-prec mir-220 Xq25 2.14E−09 Down hsa-mir-220-prec mir-220 Xq25 3.16E−05 Down hsa-mir-221-prec mir-221 Xp11.3 1.39E−05 Down hsa-mir-223-prec mir-223 Xq12-13.3 9.04E−04 Down *The correlation with fragile sites (FRA) location is as published in Calin et al., Proc Natl Acad Sci USA. 101, 2999-3004 (2004).

As indicated in the CLL vs. CD5+ B cell list of Table 10, several miRNAs located exactly inside fragile sites (miR-183 at FRA7H, miR-190 at FRA15A and miR-24-1 at FRA9D) and miR-213. The mature miR-213 molecule is expressed at lower levels in all the CLL samples, and the precursor miR-213 is reduced in expression in 62.5% of the samples. miR-16-1, at 13q14.3, which we previously reported to be down-regulated in the majority of CLL cases by microarray analysis (G. A. Calin et al., Proc Natl Acad Sc USA. 99, 15524-15529 (2002), was expressed at low levels in 45% of CLL samples. An identical mature miR-16 exists on chromosome 3; because the 40-mer oligonucleotide for both miR-16 sequences from chromosome 13 (miR-16-1) and chromosome 3 (miR-16-2) exhibit the same 23-mer mature sequence, very similar profiles were observed. However, since we observed very low levels of miR-16-2 expression in CLL samples by Northern blot, the expression observed is mainly contributed by miR-16-1. The other miRNA of 13q14.3, miR-15a, was expressed at low levels in ˜25% of CLL cases. Overall, these data demonstrate that CLL is a malignancy with extensive alterations of miRNA expression.

Validation of the microarray data was supplied for four miRNAs by Northern blot analyses: miR-16-1, located within the region of deletion at 13q14.3, miR-26a, on chromosome 3 in a region not involved in the pathogeneses of CLL, and miR-206 and miR-223 that are down-regulated (see above) in the majority of samples. For all four miRNAs, the Northern blot analyses confirmed the data obtained using the microarray. We also performed real-time PCR to measure expression levels of precursor molecules for five genes (miR-15a, miR-16-1, miR-18, miR-21, and miR-30d) and we found results concordant with the chip data.

Unsupervised hierarchical clustering generated two clearly distinguishable miRNA signatures within the set of CLL samples, one closer to the miRNA expression profile observed in human leukocytes and the other clearly different (FIG. 3). A list of the microRNAs differentially expressed between the two main CLL clusters is given in Table 11. The name of each miRNA is as in the miRNA Registry. The disregulation of either active molecule or precursor is specified in the name. The location in minimally deleted or minimally amplified or breakpoint regions or in fragile sites is presented. The top 25 differentially expressed miRNA in these two signatures (at p<0.001) include genes known or suggested to be involved in cancer. The precursor of miR-155 is over-expressed in the majority of childhood Burkitt's lymphoma (M. Metzler, M. Wilda, K. Busch, S. Viehmann, A. Borkhardt, Genes Chromosomes Cancer. 39, 167-9. (2004)), miR-21 is located at the fragile site FRA17B (G. A. Calin et al., Proc Natl Acad Sci US A. 101, 2999-3004. (2004)), miR-26a is at 3p21.3, a region frequently deleted region in epithelial cancers, while miR-92-1 and miR-17 are at 13q32, a region amplified in follicular lymphoma (Id.).

TABLE 11 microRNAs differentially expressed between the two main CLL clusters*. Oligonucleotide miRNA Chr location P-value Cancer-associated genomic regions hsa-miR-017-precNo2 miR-17-prec 13q31 0.00000000 Amp - Folicular Ly/Del - HCC hsa-miR-020-prec miR-20 13q31 0.00000000 Amp - Folicular Ly/Del - HCC hsa-miR-103-2-prec miR-103-2 20p13 0.00000001 hsa-miR-030d-precNo2 miR-30d-prec 08q24.2 0.00000002 hsa-miR-106-prec-X miR-106 Xq26.2 0.00000006 Del - advanced ovarian ca. hsa-miR-026b-prec miR-26b 02q35 0.00000006 hsa-miR-103-prec-5 = 103-1 miR-103-1 05q35.1 0.00000006 hsa-miR-025-prec miR-25 07q22 0.00000007 FRA7F hsa-miR-030a-precNo1 miR-30a 06q12-13 0.00000008 hsa-miR-021-prec-17No1 miR-21 17q23.2 0.00000008 Amp - Neuroblastoma; FRA17B hsa-miR-107-prec-10 miR-107 10q23.31 0.00000008 hsa-miR-092-prec-13 = 092-1No2 miR-92-1-prec 13q31 0.00000024 Amp - Follicular Ly. hsa-miR-027a-prec miR-27a 19p13.2 0.00000024 hsa-miR-023a-prec miR-23a 19p13.2 0.00000032 hsa-miR-092-prec-X = 092-2 miR-92-2 Xq26.2 0.00000040 Del - Advanced Ovarian ca. hsa-miR-030b-precNo1 miR-30b 08q24.2 0.000004 hsa-miR-026a-precNo1 miR-26a 03p21 0.000009 Del - Epithelial malignancies hsa-miR-093-prec-7.1 = 093-1 miR-93-1 07q22 0.000009 Amp - Folicular Ly/Del - HCC; FRA7F hsa-miR-194-precNo1 miR-194 01q41 0.000015 FRA1H hsa-miR-155-prec miR-155 21q21 0.000028 Amp - Colon ca; Childhood Burkit Ly hsa-miR-153-2-prec miR-153-2 07q36 0.000028 t(7; 12)(q36; p13) - Acute Myeloid Leukemia hsa-miR-193-precNo2 miR-193-prec 17q11.2 0.000044 Del - Ovarian ca. hsa-miR-130a-precNo1 miR-130a 11q12 0.0001 hsa-miR-023b-prec miR-23b 09q22.1 0.0001 Del - Urothelial Ca.; FRA9D hsa-miR-030c-prec miR-30c 06q13 0.0001 hsa-miR-139-prec miR-139 11q13 0.0001 hsa-miR-144-precNo2 miR-144-prec 17q11.2 0.0001 Amp - Primary Breast ca. hsa-miR-29b-2 = 102prec7.1 = 7.2 miR-29b-2 07q32 0.0002 Del - Prostate ca agressiveness; FRA7H hsa-miR-125a-precNo2 miR-125a-prec 19q13.4 0.0002 hsa-miR-224-prec miR-224 Xq28 0.0002 hsa-miR-211-precNo1 miR-211 Xp11.3 0.0002 Del - Malignant Mesothelioma. hsa-miR-221-prec miR-221 Xp11.3 0.0002 hsa-miR-191-prec miR-191 03p21 0.0002 hsa-miR-018-prec miR-18 13q31 0.0003 Amp - Follicular Lymphoma hsa-miR-203-precNo2 miR-203-prec 14q32.33 0.0004 Del - Nasopharyngeal ca. hsa-miR-217-precNo2 miR-217-prec 02p16 0.0004 hsa-miR-204-precNo2 miR-204-prec 09q21.1 0.0004 hsa-miR-199a-1-prec miR-199a-1 19p13.2 0.0005 hsa-miR-128b-precNo1 miR-128b 03p22 0.0005 hsa-miR-102-prec-1 miR-102 01q32.2-32.3 0.0005 Del - Prostate ca agressiveness hsa-miR-140No2 miR-140-prec 16q22.1 0.0006 hsa-miR-199a-2-prec miR-199a-2 01q23.3 0.0007 hsa-miR-010b-precNo2 miR-10b-prec 02q31 0.0008 hsa-miR-029a-2No1 miR-29a-2 07q32 0.0008 Del - Prostate ca agressiveness; FRA7H hsa-miR-125a-precNo1 miR-125a 19q13.4 0.0010 hsa-miR-204-precNo1 miR-204 09q21.1 0.0011 hsa-miR-181a-precNo1 miR-181a 09q33.1-34.13 0.0014 Del - Bladder ca hsa-miR-188-prec miR-188 Xp11.23-p11.2 0.0014 hsa-miR-200a-prec miR-200a 01p36.3 0.0014 hsa-miR-024-2-prec miR-24-2 19p13.2 0.0014 hsa-miR-134-precNo2 miR-134-prec 14q32 0.0016 Del - Nasopharyngeal ca. hsa-miR-010a-precNo2 miR-10a-prec 17q21.3 0.0018 hsa-miR-029c-prec miR-29c 01q32.2-32.3 0.0021 hsa-miR-010a-precNo1 miR-10a 17q21.3 0.0022 hsa-let-7d-v2-precNo1 let-7d-v2 12q14.1 0.0022 Del - Urothelial carc; FRA9D hsa-miR-205-prec miR-205 01q32.2 0.0023 hsa-miR-129-precNo1 miR-129 07q32 0.0023 Del - Prostate ca agressiveness hsa-miR-032-precNo2 miR-32-prec 09q31.2 0.0026 Del - Lung ca.; FRA9E hsa-miR-187-precNo2 miR-187-prec 18q12.1 0.0035 hsa-miR-125b-2-precNo1 miR-125b-2 21q11.2 0.0036 Del - Lung ca.(MA17) hsa-miR-181c-precNo1 miR-181c 19p13.3 0.0036 hsa-miR-132-precNo2 miR-132-prec 17p13.3 0.0036 Del - HCC hsa-miR-215-precNo1 miR-215 01q41 0.0036 FRA1H hsa-miR-136-precNo1 miR-136 14q32 0.0036 Del - Nasopharyngeal ca. hsa-miR-030a-precNo2 miR-30a-prec 06q12-13 0.0040 hsa-miR-100-1/2-prec miR-100 11q24.1 0.0040 Del - 0varian Ca.; FRA11B hsa-miR-218-2-precNo1 miR-218-2 05q35.1 0.0040 hsa-miR-193-precNo1 miR-193 17q11.2 0.0052 Del - Ovarian ca. hsa-miR-027b-prec miR-27b 09q22.1 0.0058 Del - Bladder ca; FRA9D hsa-miR-220-prec miR-220 Xq25 0.0065 hsa-miR-024-1-precNo1 miR-24-1 09q22.1 0.0065 Del - Urothelial ca. hsa-miR-019a-prec miR-19a 13q31 0.0071 Amp - Follicular Ly hsa-miR-196-2-precNo1 miR-196-2 12q13 0.0082 FRA12A hsa-miR-022-prec miR-22 17p13.3 0.0086 Del - HCC hsa-miR-183-precNo2 miR-183-prec 07q32 0.0086 Del - Prostate ca agressiveness; FRA7H hsa-miR-128a-precNo2 miR-128a-prec 02q21 0.0105 Del - Gastric Ca hsa-miR-203-precNo1 miR-203 14q32.33 0.0109 Del - Nasopharyngeal ca. hsa-miR-033b-prec miR-33b 17p11.2 0.0109 Amp - Breast ca. hsa-miR-030d-precNo1 miR-30d 08q24.2 0.0111 hsa-miR-133a-1 miR-133a-1 18q11.1 0.0119 hsa-miR-007-3-precNo2 miR-7-3-prec 22q13.3 0.0128 hsa-miR-021-prec-17No2 miR-21-prec 17q23.2 0.0131 Amp - Neuroblastoma hsa-miR-208-prec miR-208 14q11.2 0.0134 Del - Malignant Mesothelioma hsa-miR-154-prec1No2 miR-154-prec 14q32 0.0146 Del - Nasopharyngeal ca. hsa-miR-141-precNo2 miR-141-prec 12p13 0.0154 hsa-miR-024-1-precNo2 miR-024-1-prec 09q22.1 0.0169 Del - Urothelial carc; FRA9D hsa-miR-128a-precNo1 miR-128a 02q21 0.0170 Del - Gastric Ca hsa-miR-184-precNo2 miR-184-prec 15q24 0.0219 hsa-miR-019b-2-prec miR-19b-2 13q31 0.0302 hsa-miR-132-precNo1 miR-132 17p13.3 0.0303 Del - Hepatocellular ca. (HCC) hsa-miR-127-prec miR-127 14q32 0.0326 Del - Nasopharyngeal ca. hsa-miR-202-prec miR-202 10q26.3 0.0333 hsa-let-7g-precNo2 let-7g-prec 03p21.3 0.0350 Del - Lung Ca., Breast Ca. hsa-miR-222-precNo1 miR-222 Xp11.3 0.0351 hsa-miR-009-1No2 miR-009-1-prec 05q14 0.0382 hsa-miR-136-precNo2 miR-136-prec 14q32 0.0391 Del - Nasopharyngeal ca. hsa-miR-010b-precNo1 miR-10b 02q31 0.0403 hsa-miR-223-prec miR-223 Xq12-13.3 0.0407 *The location in minimally deleted or minimally amplified or breakpoint regions or in fragile sites is presented. HCC—Hepatocellular ca.; AML—acute myeloid leukemia.

The two clusters may be distinguished by at least one clinico-biological factor. A high difference in the levels of ZAP-70 characterized the two groups: 66% (6/9) patients from the first cluster vs. 25% (4/16) patients from the second one have low levels of ZAP-70 (<20%) (P=0.04 at chi test) (Table 9). The mean value of ZAP-70 was 19% (±31% S.D.) vs. 35% (±30% S.D.), respectively or otherwise the two clusters can discriminate between patients who express and who do not express this protein (at levels <20% ZAP-70 is considered as non-expressed) (Table 9). ZAP-70 is a tyrosine kinase, which is a strong predictor of early disease progression, and low levels of expression are proved to be a finding associated with good prognosis (J. A. Orchard et al., Lancet 363, 105-11 (2004)).

The microarray data revealed specific molecular signatures predictive for subsets of CLL that differ in clinical behavior. CLL cases harbor deletions at chromosome 13q14.3 in approximately 50% of cases (F. Bullrich, C. M. Croce, Chronic Lymphoid leukemia. B. D. Chenson, Ed. (Dekker, New York, 2001)). As a single cytogenetic defect, these CLL patients have a relatively good prognosis, compared with patients with leukemia cells harboring complex cytogenetic changes (H. Dohner et al., N Engl J Med. 343, 1910-6. (2000)). It was also shown that deletion at 13q14.3 was associated with the presence of mutated immunoglobulin V_(H) (IgV_(H)) genes (D. G. Oscier et al., Blood. 100, 1177-84 (2002)), another good prognostic factor. By comparing expression data of CLL samples with or without deletions at 13q14, we found that miR-16-1 was expressed at low levels in leukemias harboring deletions at 13q14 (p=0.03, ANOVA test). We also found that miR-24-2, miR-195, miR-203, miR-220 and miR-221 are expressed at significantly reduced levels, while miR-7-1, miR-19a, miR-136, miR-154, miR-217 and the precursor of miR-218-2 are expressed at significantly higher levels in the samples with 13q14.3 deletions, respectively (Table 12). All these genes are located in different regions of the genome and differ in their nucleotide sequences, excluding the possibility of cross-hybridization. Without wishing to be bound by any theory, these results suggest the existence of functional miRNA networks in which hierarchical regulation may be present, with some miRNA (such as miR-16-1) controlling or influencing the expression of other miRNA

TABLE 12 microRNAs signatures associated with prognosis in B-CLL¹. Chr. miRNA location P-value Association Observation miR-7-1 9q21.33 0.030 13q14 normal miR-16-1 13q14.3 0.030 IGVH mutations negative 0.023 13q14 deleted miR-19a 13q31 0.024 13q14 normal miR-24-2 19p13.2 0.033 13q14 deleted miR-29c 1q32.2-32.3 0.018 IGVH mutations cluster miR- positive 29c-miR 102 miR-102 1q32.2-32.3 0.023 IGVH mutations cluster miR- positive 29c-miR 102 miR-132 17p13.3 0.033 IGVH mutations negative miR-136 14q32 0.045 13q14 normal miR-154 14q32 0.020 13q14 normal miR-186 1p31 0.038 IGVH mutations negative mir-195 17p13 0.036 13q14 deleted miR-203 14q32.33 0.026 13q14 deleted miR-217-prec 2p16 0.005 13q14 normal miR-218-2 5q35.1 0.019 13q14 normal miR-220 Xq25 0.026 13q14 deleted miR-221 Xp11.3 0.021 13q14 deleted ¹The name of each miRNA is as in miRNA Registry and the disregulation of either active molecule or precursor is specified in the name.

The expression of mutated IgV_(H) is a favorable prognostic marker (D. G. Oscier et al., Blood. 100, 1177-84 (2002)). We found a distinct miRNA signature composed of 5 differentially expressed genes (miR-186, miR-132, miR-16-1, miR-102 and miR-29c) that distinguished CLL samples that expressed mutated IgV_(H) gene from those that expressed unmutated IgV_(H) genes, indicating that miRNA expression profiles have prognostic significance in CLL. As a confirmation of our results is the observation that the common element between the del 13q14.3-related and the IgV_(H)-related signatures is miR-16-1. This gene is located in the common deleted region 13q14.3 and the presence of this particular deletion is associated with good prognosis. Therefore, miRNAs expand the spectrum of adverse prognostic markers in CLL, such as expression of ZAP-70, unmutated IgV_(H), CD38, deletion at chromosome 11q23, or loss or mutation of TP53.

Example 12 Identification of miRNA Signature Profiles Associated with Prognostic Factors and Disease Survival in B-Cell Chronic Leukemia Samples

Introduction

Knowing that the expression profile of miRNome, the full complement of microRNAs in a cell, is different between malignant CLL cells and normal corresponding cells, we asked whether microarray analysis using the miRNACHIP could reveal specific molecular signatures predictive for subsets of CLL that differ in clinical behavior. The miRNome expression in 94 CLL samples was determined utilizing the microchip of Example 10. miRNA expression profiles were analyzed to determine if distinct molecular signatures are associated with the presence or absence of two prognostic markers, ZAP-70 expression and mutation of the IgV_(H) gene. The microarray data revealed that two specific molecular signatures were associated with the presence or absence of each of these markers. An analysis of expression profiles from Zap-70 positive/IgV_(H) unmutated (Umut) vs. Zap-70 negative/IgV_(H) mutated (Mut) CLL samples revealed a unique signature of 17 genes that can distinguish these two subsets. Our results indicate that miRNA expression profiles have prognostic significance in CLL.

Materials and Methods

Patient Samples and Clinical Database. 94 CLL samples were used for this study, which were obtained after informed consent from patients diagnosed with CLL at the CLL Research Consortium institutions (L. Z. Rassenti et al. N. Engl. J. Med. 351(9):893-901 (2004)). Briefly, blood was obtained from CLL patients and mononuclear cells were isolated through Ficoll/Hypaque gradient centrifugation (Amersham Pharmacia Biotech) and processed for RNA extraction according to described protocols (G. A. Calin et al., Proc. Natl. Acad. Sc. U.S.A. 99, 15524-15529 (2002)). For each sample, clinical and biological information, such as sex, age at diagnosis, Rai stage, presence/absence of treatment, time between diagnosis and therapy, ZAP-70 expression, and IgV_(H) gene mutation status, were available and are described in Table 13.

TABLE 13 Characteristics of patients analyzed with the miRNACHIP. Characteristic Value Male sex - no. of patients (%) 58 (61.7) Age at diagnosis - years median 57.3 range 38.2 Therapy begun No No. of patients 53 Time since diagnosis - months 87.07 Yes No. of patients 41 Time between diagnosis & therapy - months 40.27 ZAP-70 level ≦20% 48 >20% 46 IgV_(H) Unmutated (≧98% homology) 57 Mutated (<98% homology) 37

RNA Extraction and Northern Blots. Total RNA isolation and RNA blotting were performed as described (G. A. Calin et al., Proc Proc. Natl. Acad. Sc. U.S.A. 99, 15524-15529 (2002)).

Microarray Experiments. Microarray experiments were performed as described in Example 11. Of note, for 76 microRNAs on the miRNACHIP, two specific oligonucleotides were synthesized—one identifying the active 22 nucleotide part of the molecule and the other identifying the 60-110 nucleotide precursor. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix.

Data Analysis. After construction of the expression table with Genespring, data normalization was performed by using Bioconductor package. Analyses were carried out using the PAM package (Prediction Analysis of Microarrays) and SAM (Significance Analysis of Microarrays) software. The data were confirmed by Northern blotting for 4 microRNAs in 20 CLL samples, each. All data were submitted using MIAMExpress to the Array Express database.

Analysis of ZAP-70 and Sequence analysis of expressed IgV_(H). Analyses were performed as described previously (L. Z. Rassenti et al. N. Engl. J. Med. 351(9):893-901 (2004)). Briefly, ZAP-70 expression was assessed by immunoblot analysis and flow cytometry, while the analysis of expressed IgV_(H) was performed by direct sequencing.

Results

Comparison of miRNA expression in ZAP-70 positive vs. ZAP-70 negative CLL cells. Using 20% as a cutoff for defining ZAP-70 positivity, we constructed two classes that were constituted of 48 ZAP-70-negative and 46 ZAP-70-positive CLL samples, respectively. The analyses carried out using the PAM package identified an expression signature composed of 14 microRNAs (14/190 miRNAs on chip, 7.35%) with a PAM score >±0.02 (Table 14). Using the expression of these microRNAs, it is possible to predict with a low misclassification error (about 0.2 at cross-validation) the type of ZAP-70 expression in a patient's malignant B cells.

Comparison of miRNA expression in IgV_(H) positive vs. IgV_(H) negative CLL cells. The expression of a mutated IgV_(H) gene is a favorable prognostic marker (D. G. Oscier et al., Blood. 100, 1177-84 (2002)). ZAP-70 expression is well correlated with the status of the IgV_(H) gene. Therefore, we asked whether a specific microRNA signature can predict the mutated (Mut) vs. unmutated (Umut) status of this gene. Using the 98% cutoff for homology with germ-line IgV_(H), we identified two groups of patients composed of 37 Umut(≧98% homology) and 57 Mut (<98% homology). Based on this analysis, 12 microRNAs can be used to correctly predict the Umut vs. Mut status of the gene with a low error (0.02) (Table 14). All of these genes are included in the previous signature.

Comparison of miRNA expression in Zap-70 positive/IgV_(H) Umut vs. Zap-70 negative/IgV_(H) Mut CLL cells. We divided the 94 CLL cases into 4 groups (Zap-70 positive/IgV_(H) Umut, Zap-70 positive/IgV_(H) Mut, Zap-70 negative/IgV_(H) Umut and Zap-70 negative/IgV_(H) Mut), and have found, using the PAM package, that the same unique signature composed of 17 genes can discriminate between the two main groups of patients, Zap70 positive/IgV_(H) Umut and Zap-70 negative/IgV_(H) Mut. In this case, we observed the lowest classification error (0.015 at cross validation). Only one patient was Zap-70 negative and IgV_(H) Umut, and therefore was not used in the classification. When the remaining three classes were analyzed, the 10 patients belonging to the Zap-70 positive/IgV_(H) Mut class were always misclassified, which indicates that there are no microRNAs on the miRNACHIP that can compose a different signature. The same unique signature was identified using another algorithm of microarray analysis, SAM, thereby confirming the reproducibility of our results. These results indicate that miRNA expression profiles have prognostic significance in CLL and can be used for diagnosing the disease state of a particular cancer by determining whether or not a given profile is characteristic of a cancer associated with one or more adverse prognostic markers.

TABLE 14 A miRNA signature associated with prediction factors and disease survival in CLL patients. Short vs. IgV_(H) Mut Zap70+/IgV_(H) Long ZAP-70+ vs. Umut vs. time to Signature vs. IgV_(H) Zap70−/IgV_(H) initial component Zap-70− Umut Mut therapy Observation mir-015a −0.0728 NA −0.0372 vs. NA cluster 15a/16-1 vs. 0.076 0.0485 del CLL, prostate ca. 13q13.4 (G. A. Calin et al., Proc. Natl. Acad. Sic. USA. 99, 15524-15529 (2002)) mir-016-1 −0.1396 −0.0852 −0.1444 vs. NA del CLL, prostate vs. vs. 0.1312 0.1886 ca. 13q13.4 (G. A. Calin 0.1457 et al., Proc. Natl. Acad. Sci. USA. 99, 15524-15529 (2002)) mir-016-2 −0.1615 −0.0969 −0.1619 vs. NA identical 16-1/16-2 vs. vs. 0.1493 0.2113 0.1685 mir-023a −0.0235 0.0647 vs. −0.0748 vs. 0.0587 cluster 23a/24-2 vs. 0.0997 0.0977 vs. −0.019 0.0245 mir-023b −0.0658 −0.0663 −0.0909 vs. 0.0643 cluster 24-1/23b vs. vs. 0.1021 0.1187 vs. −0.0208 FRA 9D; del 0.0686 Urothelial ca. 9q22. (G. A Calin et al. Proc. Natl. Acad. Sci. U.S.A. 101(32): 11755-60 (2004)) mir-024-1 NA −0.042 vs. −0.0427 vs. NA FRA 9D; del 0.0648 0.0558 Urothelial ca. 9q22 (ref (G. A. Calin et al. Proc. Natl. Acad. Sci. U.S.A. 101(32): 11755-60 (2004)) mir-024-2 NA NA −0.0272 vs. 0.0696 0.0355 vs. −0.0225 mir-029a 0.0806 0.0887 vs. 0.1139 vs. −0.1487 NA cluster 29a/29b-1 vs. −00842 −0.1367 FRA7H; del Prostate ca. 7q32 (G. A. Calin et al. Proc. Natl. Acad. Sci. U.S.A. 101(32): 11755-60 (2004)) mir-29b-2 0.1284 0.1869 vs. 0.2065 vs. −0.2696 NA 1q32.2-32.3 vs. −0.134 −0.2879 mir-029c 0.1579 0.1846 0.2174 vs. −0.2839 −0.0221 vs. −0.1648 vs. −0.2844 vs. 0.0072 mir-146 −0.1518 −0.1167 −0.1803 vs. 0.07 vs. vs. 0.1798 0.2354 vs. −0.0227 0.1584 mir-155 −.0.1015 −0.0743 −0.1155 vs. 0.1409 amp child Burkitt's vs. vs. 0.1145 0.1508 vs. −0.0456 lymphoma, colon 0.1059 ca. (M. Metzler et al. Genes Chromosomes Cancer. Feb; 39(2): 167-9 (2004)) and (M. Z. Michael et al. Mol Cancer Res. 1(12): 882-91 (2003)). mir-181a −0.0473 NA −0.0279 vs. 0.1862 Up-regulated in vs. 0.0364 vs. −0.0603 differentiated B ly 0.0494 (C. Z. Chen et al. Science. 303(5654): 83-6 (2004)). mir-195 −0.0679 NA −0.053 vs. NA vs. 0.0692 0.0708 mir-221 −0.0812 −0.0839 −0.1157 vs. 0.0343 cluster 221/222 vs. vs. 0.1292 0.1511 vs. −0.0111 0.0848 mir-222 NA NA −0.022 vs. 0.0458 0.0288 vs. −0.0148 mir-223 0.0522 0.1036 vs. 0.1056 vs. −0.1379 NA Normally vs. −0.0544 −0.1596 expression restricted to myeloid lineage (C. Z. Chen et al. Science. 303(5654): 83-6 (2004)). Note: ZAP-70 negative = ZAP-70 expression ≦20%; ZAP-70 positive = ZAP-70 expression >20%; IgV_(H) unmutated = homology ≧98%; IgV_(H) mutated = homology <98%. The numbers indicate the PAM scores in the two classes (n score and y score). mir-29b-2 was previously named mir-102.

Association between miRNA expression and time to initial therapy. Treatment of patients according to the National Cancer Institute Working Group criteria (B. D. Cheson et al. Blood. 87(12):4990-7 (1996)) was performed when symptomatic or progressive disease developed. Of the 94 patients studied, 41 had initiated therapy (Table 13). We examined the relationship between the expression of 190 microRNA genes and either the time from diagnosis to initial therapy (for patients that have begun treatment) or from the time of diagnosis to the present (for those patients who haven't begun treatment), collectively representing the total group of 94 patients in the study. We found that the expression profile generated by a spectrum of 9 microRNAs, all components of the unique signature, can differentiate between two subsets of patients in the group of 94 tested—one subset with a short interval from diagnosis to initial therapy and the second subset with a significantly longer interval (see Table 14 and FIG. 5). The significance of Kaplan-Meier curves improves if we restrict the analyses to the two main groups of 83 patients (the Zap-70 positive/IgV_(H) Umut and Zap-70 negative/IgV_(H) Mut groups) or if we use only the 17 microRNAs from the signature (P decreases from <0.01 to P<0.005 and P<0.001, respectively). All of the microRNAs which can predict the time to initial therapy, with the exception of mir-29c, are overexpressed in the group characterized by a short interval from diagnosis to initial therapy.

Example 13 Identification of sequence alterations in miR genes associated with CLL

Introduction

Using tumor DNA from CLL samples, we screened more than 700 kb of tumor DNAs (mean 39 patients/miRNA for mean 500 bp/miRNA) for sequence alterations in each of 35 different miR genes. Very rare polymorphisms or tumor specific mutations were identified in 4 of the 39 CLL cases, affecting one of three different miR genes: miR-16-1, miR-27b and miR-206. In two other miR genes, miR-34b and miR-100, polymorphisms were identified in both CLL and normal samples with similar frequencies.

Materials and Methods

Detection of microRNA mutations. Thirty-five miR genes were analyzed for the presence of a mutation, including 16 members of the miR expression signature identified in Example 12 (mir-15a, mir-16-1, mir-23a, mir-23b, mir-24-1, mir-24-2, mir-27a, mir-27b, mir-29b-2, mir-29c, mir-146, mir-155, mir-181a, mir-221, mir-222, mir-223) and 19 other miR genes selected randomly (let-7a2, let-7b, mir-21, mir-30a, mir-30b, mir-30c, mir-30d, mir-30e, mir-32, mir-100, mir-108, mir-125b1, mir-142-5p, mir-142-3p, mir-193, mir-181a, mir-206, mir-213 and mir-224).

The algorithm for screening for miR gene mutations in CLL samples was performed as follows: the genomic region corresponding to each precursor miRNA from either 39 CLL samples or 3 normal mononuclear cell samples from healthy individuals was amplified, including at least 50 base pairs in the 5′ and 3′ extremities. For the miRNAs located in clusters covering less than one kilobase, the entire corresponding genomic region was amplified and sequenced using the Applied Biosystems Model 377 DNA sequencing system (PE, Applied Biosystems, Foster City, Calif.). When a deviation from the normal sequence was found, a panel of blood DNAs from 95 normal individuals was screened to confirm that the deviation represented a polymorphism. If the sequencing data were normal, an additional panel of 37 CLL cases was screened to determine the frequency of mutations in a total of 76 cancer patients. If additional mutations were found, another set of 65 normal DNAs was screened, to assess the frequency of the specific alteration in a total of 160 normal samples.

In vivo studies of mir-16-1 mutant effects. We constructed two mir-16-1/mir-15a expression vectors—one containing an 832 base pair genomic sequence that included both mir-16-1 and mir-15a, and another nearly identical construct containing the C to T mir-16-1 substitution, as shown in SEQ ID NO. 642—by ligating the relevant open reading frame in a sense orientation into the mammalian expression vector, pSR-GFP-Neo (OligoEngine, Seattle, Wash.). These vectors are referred to as mir-16-1-WT and mir-16-1-MUT, respectively. All sequenced constructs were transfected into 293 cells using Lipofectamine 2000 according to the manufacturer's protocol (Invitrogen, Carlsbad, Calif.). The expression of both mir-16-1-WT and mir-16-1-MUT constructs was assessed by Northern blotting as previously described (G. A. Calin et al., Proc. Natl. Acad. Sc. U.S.A. 99, 15524-15529 (2002)).

Results

Very rare polymorphisms or tumor specific mutations were identified in 4 of the 39 CLL cases, affecting one of three different miR genes: miR-16-1, miR-27b and miR-206 (Tables 15 and 16). In two other miR genes, miR-34b and miR-100, polymorphisms were identified in both CLL and normal samples with similar frequencies (see Tables 15, 16 and Results section below).

TABLE 15 Genetic variations in the genomic sequences of miR genes in CLL patients. Other miRNA miRNA Mutation CLL (%) allele Normals CHIP Observation mir-16-1 C to T 2/76 (2.6) Deleted 0/160 (0) Reduced Heterozygous in (see SEQ ID (FISH, expression normal cells NO. 642) LOH) from both patients; Previous breast cancer; Mother died with CLL; sister died with breast cancer. mir-27b G to A 1/39 (2.6) Normal 0/98 (0)  Normal (see SEQ ID expression NO. 646) mir-206 G to A 1/39 (2.6) Normal NA NA (see SEQ ID NO. 647) mir-100 G to A 17/39 (43.5) Normal 2/3 NA (see SEQ ID NO. 644)

TABLE 16 Sequences showing genetic variations in the miR genes of CLL patients. SEQ Precursor Sequence ID Name (5′ to 3′) NO. hsa-mir-16- GTCAGCAGTGCCTTAGCAGCACGTAAATATTGGCG 641 1-normal TTAAGATTCTAAAATTATCTCCAGTATTAACTGTG CTGCTGAAGTAAGGTTGACCATACTCTAC hsa-mir-16- GTCAGCAGTGCCTTAGCAGCACGTAAATATTGGCG 642 1-MUT TTAAGATTCTAAAATTATCTCCAGTATTAACTGTG CTGCTGAAGTAAGGTTGACCATACT T TAC hsa-mir-100 CCTGTTGCCACAAACCCGTAGATCCGAACTTGTGG 643 TATTAGTCCGCACAAGCTTGTATCTATAGGTATGT GTCTGTTAGGCAATCTCACGGACC hsa-mir- CCTGTTGCCACAAACCCGTAGATCCGAACTTGTGG 644 100-MUT TATTAGTCCGCACAAGCTTGTATCTATAGGTATGT GTCTGTTAGGCAATCTCAC A GACC hsa-mir- ACCTCTCTAACAAGGTGCAGAGCTTAGCTGATTGG 645 27b-normal TGAACAGTGATTGGTTTCCGCTTTGTTCACAGTGG CTAAGTTCTGCACCTGAAGAGAAGGTGAGATGGGG ACAGTTAAGTTGGAGCCGCTGGGGCAGAGGCCGTT GCTGACGGGC hsa-mir- ACCTCTCTAACAAGGTGCAGAGCTTAGCTGATTGG 646 27b-MUT TGAACAGTGATTGGTTTCCGCTTTGTTCACAGTGG CTAAGTTCTGCACCTGAAGAGAAGGTGAGATGGGG ACAGTTAAGTTGGAGCCGCTGGGGCAGAGGCCGTT GCTGAC A GGC has-mir-206 TGCTTCCCGAGGCCACATGCTTCTTTATATCCCCA 230 TATGGATTACTTTGCTATGGAATGTAAGGAAGTGT GTGGTTTCGGCAAGTG has-mir- TGCTTCCCGAGGCCACATGCTTCTTTATATCCCCA 647 206-MUT TATGGATTACTTT A CTATGGAATGTAAGGAAGTGT GTGGTTTCGGCAAGTG hsa-mir- GTGCTCGGTTTGTAGGCAGTGTCATTAGCTGATTG 648 34b-normal TACTGTGGTGGTTACAATCACTAACTCCACTGCCA TCAAAACAAGGCACAGCATCACCGCCG hsa-mir- GTGCTCGGTTTGTAGGCAGTGTCATTAGCTGATTG 650 34b-MUT TACTGTGGTGGTTACAATCACTAACTCCACTGCCA TCAAAACAAGGCACAGCATCACC A CCG Note:    Each mutation/polymorphism is underlined and indicated in bold in the sequences marked “MUT”. 

The miR-16-1 gene is located at 13q13.4. In 2 CLL patients out of 76 screened (2.6%), we found a homozygous C to T polymorphism (compare SEQ ID NO: 641 to SEQ ID NO: 642; Table 16), which is located in a 3′ region of the miR-16-1 precursor (FIG. 7C) with strong conservation in all of the primates analyzed (E. Berezikov et al., Cell 120(1):21-4 (2005)), suggesting that this polymorphism has functional implications. By RT-PCR and Northern blotting we have shown that the precursor miRNA includes the 3′ region harboring the base substitution. Both patients have a significant reduction in mir-16-1 expression in comparison with normal CD5+ cells by miRNACHIP and Northern blotting (FIG. 6, FIG. 7D). Further suggesting a pathogenic role, by FISH and LOH, we found a monoallelic deletion at 13q14.3 in the majority of examined cells. This substitution was not found in any of 160 normal control samples (p<0.05 using chi square analysis). In both patients, the normal cells from mucal mucosa were heterozygous for this abnormality. Therefore, this change is a very rare polymorphism or a germ-line mutation. In support of the latter is the fact that one of the patients has two relatives (mother and sister) who have been diagnosed with CLL and breast cancer, respectively. Therefore, this family fulfills the minimal criteria for “familial” CLL, i.e., two or more cases of B-CLL in first-degree living relatives (N. Ishibe et al., Leuk Lymphoma 42(1-2):99-108 (2001)).

To identify a possible pathogenic effect for this substitution, we inserted both the wild-type sequence of the mir-15a/mir-16-1 cluster, as well as the mutated sequence, into separate expression vectors. We transfected 293 cells, which have a low endogenous expression of this cluster. As a control, 293 cells transfected with an empty vector were tested. The expression levels of both mir-15a and mir-16-1 were significantly reduced in transfectants expressing the mutant construct in comparison to transfectants expressing the wild-type construct (FIG. 7E). The level of expression in transfectants expressing the mutant construct was comparable with the level of endogenous expression in 293 cells (FIG. 7E). Therefore, we conclude that the C to T change in miR-16-1 affects the processing of the pre-miRNA in mature miRNA.

The miR-27b gene is located on chromosome 9. A heterozygous mutation caused by a G to A change in the 3′ region of the miR-27b precursor (compare SEQ ID NO: 645 to SEQ ID NO: 646; Table 16), but within the transcript of the 23b-27b-24-1 cluster, was identified in one out of 39 CLL samples. miRCHIP analysis indicated that miR-27b expression was reduced in this sample. This change has not been found in any of the 98 normal individuals screened to date.

The miR-34b gene is located at 11q23. Four CLL patients out of 39 carried two associated polymorphisms, a G to A polymorphism, as shown in SEQ. ID NO. 650, and a T to G polymorphism located in the 3′ region of the miR-34b precursor. Both polymorphisms were within the transcript of the mir-34b-mir-34c cluster. One patient was found to be homozygous (presenting by FISH heterozygous abnormal chromosome 11q23), while the other three were heterozygous for the polymorphisms. The same frequency of mutation was found in 35 normal individuals tested.

Example 14 Identification of Abnormalities in the Genomic Sequences of MiR Genes Associated with CLL

Introduction

Abnormally expressed cancer genes are frequently targets for genetic abnormalities, e.g., mutations that can either activate or inactivate their function. Therefore, we screened 42 microRNAs for germline or somatic mutations.

Materials and Methods

Detection of microRNA gene mutations.

The genomic region corresponding to each precursor miRNA, including at least 50 additional base pairs (bp) in the 5′ and 3′ extremities (i.e., flanking sequences), was amplified from 40 CLL samples and normal mononuclear cell samples from 3 healthy individuals. For the miRNAs located in clusters that were less than one kilobase (kb) in length, the entire corresponding genomic region was amplified and sequenced using the Applied Biosystems Model 377 DNA sequencing system (PE, Applied Biosystems, Foster City, Calif.). When a deviation from the normal sequence was found, a panel of blood DNAs from 160 normal individuals, as well as an additional panel of 35 CLL cases (total of 75 leukemia patients), were screened to confirm polymorphisms. All subjects were Caucasian, as indicated by medical records of CLL patients and information obtained during an interview for control patients. For 46 CLL patients, personal and/or familial cancer history was known. Forty-two miR genes were screened for germline or somatic mutations, including 15 members of the specific signature identified in Example 12, or members of the same cluster: miR-15a, miR-16-1, miR-23a, miR-23b, miR-24-1, miR-24-2, miR-27a, miR-27b, miR-29b-2, miR-29c, miR-146, miR-155, miR-221, miR-222, miR-223, as well as 27 other microRNAs that were selected randomly: let-7a2, let-7b, miR-17-3p, miR-17-5p, miR-18, miR-19a, miR-19b-1, miR-20, miR-21, miR-30b, miR-30c-1, miR-30d, miR-30e, miR-32, miR-100, miR-105-1, miR-108, miR-122, miR-125b-1, miR-142-5p, miR-142-3p, miR-193, miR-181a, miR-187, miR-206, miR-224, miR-346.

Results

Germline or somatic mutations were identified in miRNA genomic regions in 11 out of 75 (15%) CLL samples. Five different miRNAs were affected by mutations (5/42 miR genes analyzed, 12%): miR-16-1, miR-27b, miR-206, miR-29b-2 and miR-187. None of these mutations were found in a set of 160 individuals without cancer (p<0.0001) (see Table 17). The positions of the various mutations are shown relative to the position of the miR gene in FIG. 7A. All the abnormalities are localized in regions that are transcribed, as shown by RT-PCR (FIG. 7B). Eight of the 11 (73%) patients with abnormal miRNA sequences have a known personal or familial history of CLL or other hematopoietic or solid tumors (Table 17). Sequences containing the identified miR gene mutations, as well as their corresponding wild-type sequences, are shown in Table 16 for miR-16-1 and miR-27b and in Table 18 for miR-29b-2, miR-187 and miR-206. Two mutations were identified in miR-29b-2 and miR-206 (labeled MUT1 and MUT2, respectively, in Table 18). In addition, a polymorphism was detected in both CLL and normal samples with similar frequencies for three other miR genes: miR-29c, miR-122a and miR-187 (labeled MUT2) (see Tables 17 and 18).

TABLE 17 Genetic variations in the genomic sequences of miR genes in CLL patients. miRNACHIP miRNA Location** CLL Normals expression Observations miR- Germline; 2/75 0/160 Reduced to Normal allele deleted in 16-1 pri- 15% and 40% CLL cells in both miRNA: of normal, patients (FISH, LOH). CtoT respectively For one patient: History substitution of previous breast at +7 bp in cancer; mother with CLL the 3′ (deceased); sister with flanking breast cancer (deceased). miR- Germline; 1/75 0/160 Normal Mother with throat and 27b pri- lung cancer at age 58. miRNA: G Father with lung cancer toA at age 57. substitution at +50bp in 3′ flanking sequence miR- pri- 1/75 0/160 Reduced to 75% Sister with breast cancer 29b-2 miRNA: G at age 88 (still living). to A Brother with “some type substitution of blood cancer” at age at +212 in 70. 3′ flanking sequence miR- pri- 3/75 0/160 Reduced to 80% Both patients have a 29b-2 miRNA: A family history of insertion at unspecified cancer. +107 in 3′ flanking sequence miR- pri- 1/75 0/160 NA Unknown 187 miRNA: T to C substitution at +73 in 3′ flanking sequence miR- pre- 2/75 0/160 Reduced to 25% Prostate cancer; mother 206 miRNA: G with esophogeal cancer. to T Brother with prostate substitution cancer; sister with breast at position cancer 49 of precursor miR- Somatic; 1/75 0/160 Reduced to 25% Aunt with leukemia 206 pri- (data only for one (deceased) miRNA: pt) A to T substitution at −116 in 5′ flanking sequence miR- pri- 2/75 1/160 NA Paternal grandmother 29c miRNA: G with CLL; sister with to A breast cancer. substitution at −31 in 5′ flanking sequence miR- pre- 1/75 2/160 Reduced to 33% Paternal uncle with 122a miRNA: C colon cancer. to T substitution at position 53 of precursor miR- pre- 1/75 1/160 NA Grandfather with 187 miRNA: G polycythemia vera. to A Father has a history of substitution cancer but not at position lymphoma. 34 of precursor For each CLL patient/normal control, more than 12 kb of genomic DNA was sequenced. In total, ~627 kb of tumor DNA and about 700 kb of normal DNA was screened by direct sequencing. The positions of the mutations are reported with respect to the precursor miRNA molecule. **When normal corresponding DNA from bucal mucosa was available, the alteration was identified as germline when present or somatic when absent, respectively. FISH = fluorescence in situ hybridization; LOH = loss of heterozygosity; NA = not available.

TABLE 18 Sequences showing genetic variations in the miR genes of CLL patients. Precursor Sequence SEQ (5′ to 3′) +/− 5′ or 3′ ID Name flanking genomic sequence NO. hsa-mir-29b- CTTCTGGAAGCTGGTTTCACATGGTGGCTT 651 2-normal AGATTTTTCCATCTTTGTATCTAGCACCAT TTGAAATCAGTGTTTTAGGAGTAAGAATTG CAGCACAGCCAAGGGTGGACTGCAGAGGAA CTGCTGCTCATGGAACTGGCTCCTCTCCTC TTGCCACTTGAGTCTGTTCGAGAAGTCCAG GGAAGAACTTGAAGAGCAAAATACACTCTT GAGTTTGTTGGGTTTTGGGAGAGGTGACAG TAGAGAAGGGGGTTGTGTTTAAAATAAACA CAGTGGCTTGAGCAGGGGCAGAGG hsa-mir-29b- CTTCTGGAAGCTGGTTTCACATGGTGGCTT 652 2-MUT1 (G to A AGATTTTTCCATCTTTGTATCTAGCACCAT substitution  TTGAAATCAGTGTTTTAGGAGTAAGAATTG at +212 in 3′ CAGCACAGCCAAGGGTGGACTGCAGAGGAA flanking  CTGCTGCTCATGGAACTGGCTCCTCTCCTC sequence) TTGCCACTTGAGTCTGTTCGAGAAGTCCAG GGAAGAACTTGAAGAGCAAAATACACTCTT GAGTTTGTTGGGTTTTGGGAGAGGTGACAG TAGAGAAGGGGGTTGTGTTTAAAATAAACA CAGTGGCTTGAGCAGGGGCAGA A G hsa-mir-29b-2- CTTCTGGAAGCTGGTTTCACATGGTGGCTT 653 MUT2 (A AGATTTTTCCATCTTTGTATCTAGCACCAT insertion at  TTGAAATCAGTGTTTTAGGAGTAAGAATTG +107 in  CAGCACAGCCAAGGGTGGACTGCAGAGGAA 3′ flanking CTGCTGCTCATGGAACTGGCTCCTCTCCTC sequence) TTGCCACTTGAGTCTGTTCGAGAAGTCCAG GGAAGAA A CTTGAAGAGCAAAATACACTCT TGAGTTTGTTGGGTTTTGGGAGAGGTGACA GTAGAGAAGGGGGTTGTGTTTAAAATAAAC ACAGTGGCTTGAGCAGGGGCAGAGG hsa-mir-187- GGTCGGGCTCACCATGACACAGTGTGAGAC 654 normal CTCGGGCTACAACACAGGACCCGGGCGCTG CTCTGACCCCTCGTGTCTTGTGTTGCAGCC GGAGGGACGCAGGTCCGCAGCAGAGCCTGC TCCGCTTGTCCTGAGGGACTCGACACAGGG GACTGCACAGAGACCATGGGAAAGTCCAGG CTC hsa-mir-187- GGTCGGGCTCACCATGACACAGTGTGAGAC 655 MUT1 (T to C CTCGGGCTACAACACAGGACCCGGGCGCTG substitution   CTCTGACCCCTCGTGTCTTGTGTTGCAGCC at +73 in 3′ GGAGGGACGCAGGTCCGCAGCAGAGCCTGC flanking  TCCGCTTGTCCTGAGGGACTCGACACAGGG sequence) GACTGCACAGAGACCATGGGAAAGTCCAGG C C C hsa-mir-187- GGTCGGGCTCACCATGACACAGTGTGAGAC 656 MUT2 (G to A TCG A GCTACAACACAGGACCCGGGGCGCTG substitution  CTCTGACCCCTCGTGTCTTGTGTTGCAGCC at position 34  GGAGGGACGCAGGTCCGCAGCAGAGCCTGC of precursor) TCCGCTTGTCCTGAGGGACTCGACACAGGG GACTGCACAGAGACCATGGGAAAGTCCAGG CTC has-mir-206 GATTTAGGATGAGTTGAGATCCCAGTGATC 657 TTCTCGCTAAGAGTTTCCTGCCTGGGCAAG GAGGAAAGATGCTACAAGTGGCCCACTTCT GAGATGCGGGCTGCTTCTGGATGACACTGC TTCCCGAGGCCACATGCTTCTTTATATCCC CATATGGATTACTTTGCTATGGAATGTAAG GAAGTGTGTGGTTTCGGCAAGTG has-mir-206- GATTTAGGATGAGTTGAGATCCCAGTGATC 658 MUT1 (G to T TTCTCGCTAAGAGTTTCCTGCCTGGGCAAG substitution  GAGGAAAGATGCTACAAGTGGCCCACTTCT at position 49  GAGATGCGGGCTGCTTCTGGATGACACTGC of precursor) TTCCCGAGGCCACATGCTTCTTTATATCCC CATATGGATTACTTT T CTATGGAATGTAAG GAAGTGTGTGGTTTCGGCAAGTG has-mir-206- G T TTTAGGATGAGTTGAGATCCCAGTGATC 659 MUT2 (A to T TTCTCGCTAAGAGTTTCCTGCCTGGGCAAG substitution  GAGGAAAGATGCTACAAGTGGCCCACTTCT at −116 in 5′ GAGATGCGGGCTGCTTCTGGATGACACTGC flanking TTCCCGAGGCCACATGCTTCTTTATATCCC sequence) CATATGGATTACTTTTCTATGGAATGTAAG GAAGTGTGTGGTTTCGGCAAGTG hsa-mir-29c- CGAGGTGCAGACCCTGGGAGCACCACTGGC 660 normal CCATCTCTTACACAGGCTGACCGATTTCTC CTGGTGTTCAGAGTCTGTTTTTGTCTAGCA CCATTTGAAATCGGTTATGATGTAGGGGGA hsa-mir-29c- C+*B  A AGGTGCAGACCCTGGGAGCACCACTGGC 661 MUT (G to A CCATCTCTTACACAGGCTGACCGATTTCTC substitution   CTGGTGTTCAGAGTCTGTTTTTGTCTAGCA at −31 in 5′ CCATTTGAAATCGGTTATGATGTAGGGGGA flanking sequence) hsa-mir-122a- CCTTAGCAGAGCTGTGGAGTGTGACAATGG 662 normal TGTTTGTGTCTAAACTATCAAACGCCATTA TCACACTAAATAGCTACTGCTAGGC hsa-mir-122a- CCTTAGCAGAGCTGTGGAGTGTGACAATGG 663 MUT (C to T TGTTTGTGTCTAAACTATCAAA T GCCATTA substitution  TCACACTAAATAGCTACTGCTAGGC at position 53  of precursor) Note:    The position of each mutation/polymorphism is underlined and indicated in bold in the sequences marked “MUT”.   

Example 15 A Unique MicroRNA Signature Associated with Prognostic Factors and Disease Progression in Chronic Lymphocytic Leukemia

Introduction: In spite of extensive effort, little is known regarding the pathogenic events leading to the initiation and progression of B cell CLL, the most frequent adult leukemia in the Western world. On the contrary, several factors predicting the clinical course have been defined. CLL cells with few or no mutations in the immunoglobulin heavy-chain variable-region gene (IgV_(H)) or with high expression of the 70-kD zeta-associated protein positive (ZAP-70+) have an aggressive course, whereas patients with mutated clones or few ZAP-70+B cells have an indolent course (Chiorazzi, N., et al., N. Engl. J. Med. 352:804-815 (2005)). It was also found that genomic aberrations in CLL are important independent predictors of disease progression and survival (Dohner, H., et al., N. Engl. J. Med. 343(26):1910-1916 (2000)). However, the molecular basis of these associations is largely unknown. Here, we performed genome wide expression profiling with the miRNACHIP in a large series of CLL samples with extensive clinical data to examine whether expression of these noncoding genes is associated with factors predicting the clinical course.

Materials and Methods

Patient samples and clinical database. Samples used for this study are described in detail in Example 12.

RNA extraction, Northern blots and miRNACHIP experiments. Procedures were performed as described (Calin, G. A., et al., Proc. Natl. Acad. Sci. USA 101(32):1175-1160 (2004); Liu, C.-G., et al., Proc. Natl. Acad. Sci. USA 101(26): 9740-9744 (2004)). Briefly, labeled targets from 5 μg of total RNA was used for hybridization on each miRNACHIP microarray chip containing 368 probes in triplicate, corresponding to 245 human and mouse miRNA genes. Of note, for 76 microRNAs on the miRNACHIP two specific oligos were synthesized one identifying the active 22 nt part of the molecule and the other for the 60-110 nt precursor (Liu, C.-G., et al., Proc. Natl. Acad. Sci. USA 101(26): 9740-9744 (2004)).

Data analysis. Raw data were normalized and analyzed in GeneSpring® software version 7.2 (Silicon Genetics, Redwood City, Calif.). Expression data were median centered using both GeneSpring normalization option or Global Median normalization of the Bioconductor package, without any substantial difference. Statistical comparisons were done both using the GeneSpring ANOVA tool and the SAM software (Significance Analysis of Microarray). mRNA predictors were calculated by using PAM software (Prediction Analysis of Microarrays); the Support Vector Machine tool of GeneSpring was used for the Cross-validation and Test-set prediction. The Kaplan-Meier plot (“survival analysis” of the PAM software) was used to identify an association between miRNA expression and the time elapsing from CLL diagnosis and the beginning of therapy. miRNAs able to best separate the two groups were identified at the same time. All data were submitted using MIAMExpress to the Array Express database (accession numbers to be received upon revision). We validated the microarray data for 4 miRNAs (miR-16-1, miR-26a, miR-206 and miR-223) in 11 CLL samples and normal CD5 cells by solution hybridization detection as presented elsewhere (Calin, G. A., et al., Proc. Natl. Acad. Sci. USA 101(32):11755-11760 (2004)). Furthermore, miR-15a and miR-16-1 expression in the patients with germline mutation was confirmed by Northern blot.

Analysis of ZAP-70 and Sequence analysis of expressed IgV_(H). These experiments were performed as described in Example 12.

Results

Comparison of miRNA expression in Zap-70 positive/IgV_(H) Umut vs. Zap-70 negative/IgV_(H) Mut CLL cells. In Example 12, a unique signature that can discriminate between the two main groups of CLL patients (i.e., Zap70 positive/IgV_(H) Umut and Zap-70 negative/IgV_(H) Mut), composed of 17 genes, was identified using the PAM package. Using additional algorithms for statistical and prediction analysis (i.e., SAM and GeneSpring) to validate the PAM signature, we found that a signature composed of 13 mature microRNAs could discriminate (at P<0.01) between Zap70 positive/IgV_(H) Umut and Zap-70 negative/IgV_(H) Mut patients (Tables 19 and 20). Furthermore, the prediction made using Support Vector Machine correctly classified all patients (Table 20). The majority of miRNAs (9 out of 13) were significantly overexpressed in the group with poor prognosis. The 10 patients belonging to the Zap-70 positive and VhMut group were equally assigned to groups good or poor prognosis, suggesting either that there are no microRNAs on the miRNACHIP whose expression can distinguish these two groups, that these two groups are not different with regard to microRNA expression profiles or that the groups are too small to be correctly classified.

We used the Support Vector Machine algorithm also to predict an additional independent set of 50 CLL samples with known ZAP-70 status (Table 21). When the 13 miRNAs of the identified signature were used, the prediction was made correctly in all cases, confirming, thereby confirming our results. Also confirming the microarray specificity, as reported in Liu, C.-G., et al., Proc. Natl. Acad. Sci. USA 101(26): 9740-9744 (2004), the signature did not include very similar members of the same families, such as miR-23a (1 base difference from miR-23b) and miR-15b (four bases difference from miR-15a), while the identical mature miRNAs miR-16-1 and miR-16-2 were both identified, indicating that the chip is able to discriminate between highly similar iso forms.

TABLE 19 miRNA signature associated with prognostic factors (ZAP70 and IgVH mutations) and disease progression in CLL patients*. Group 4 Nr. Crt. Component Map P value expression** Putative targets*** Observation**** 1 miR-15a 13q14.3 0.018 high NA cluster 15a/16-1 del CLL & Prostate ca. 2 miR-195 17p13 0.017 high NA del HCC 3 miR-221 Xp11.3 0.010 high HECTD2, CDKN1B, NOVA1, cluster 221/222 ZFPM2, PHF2 4 miR-23b 9q22.1 0.009 high FNBP1L, WTAP, cluster 24-1/23b PDE4B, SATB1, SEMA6D FRA 9D; del Urothelial ca. 5 miR-155 21q21 0.009 high ZNF537, PICALM, RREB1, amp child Burkitt's lymphoma BDNF, QKI 6 miR-223 Xq12-13.3 0.007 low PTBP2, SYNCRIP, WTAP, normally expression restricted FBXW7, QKI to myeloid lineage 7 miR-29a-2 7q32 0.004 low NA cluster 29a-2/29b-1 FRA7H; del Prostate ca. 8 miR-24-1 9q22.1 0.003 high TOP1, FLJ45187, RSBN1L, cluster 24-1/23b RAP2C, PRPF4B FRA 9D; del Urothelial ca. 9 miR-29b-2 (miR-102) 1q32.2-32.3 0.0007 low NA 10 miR-146 5q34 0.0007 high NOVA1, NFE2L1, C1orf16, ABL2, ZFYVE1 11 miR-16-1 13q14.3 0.0004 high BCL2, CNOT6L, USP15, cluster 15a/16-1 PAFAH1B1, ESRRG del CLL, prostate ca. 12 miR-16-2 3q26.1 0.0003 high see miR-16-1 identical miR-16-1 13 miR-29c 1q32.2-32.3 0.0002 low NA Note: *All the members of the signature are mature miRNAs; **Group 4 includes patients with IgVh mutated and Zap-70 negative, both predictors of poor prognosis. ***top five predictions using TargetScan (Lewis, B. P., et al., Cell 120: 15-20 (2005)) were included. NA—not available; for specific gene names - see the NCBI site. ****FRA = fragile site; del = deletion; HCC = hepatocellular carcinoma; ca. = carcinoma.

TABLE 20 List of miRNAs associated with prognostic factors and disease progression in CLL patients selected by Prediction Analysis of Microarrays (PAM) and ANOVA analysis (GeneSpring)*. Nr. PAM n− y+ GeneSpring Anova crt. signature score score map signature p-value map 1 mir-222 −0.022 0.0288 Xp11.2 mir-34-prec 0.048 1p36.22 2 mir-24-2 −0.0272 0.0355 19p13.12 mir-192-2/3-prec 0.0457 11q13 3 mir-181a −0.0279 0.0364 1q32.1 mir-15a-prec 0.0353 13q14.3 4 mir-15a −0.0372 0.0485 13q14.3 mir-17 0.0257 13q31 5 mir-24-1 −0.0427 0.0558 9q22.1 mir-15a 0.018 13q14.3 6 mir-195 −0.053 0.0692 17p13 mir-195 0.0175 17p13 7 mir-23a −0.0748 0.0977 19p13.12 mir-213-prec 0.0153 1q31.3-q32.1 8 mir-23b −0.0909 0.1187 9q22.1 mir-221 0.0105 Xp11.3 9 mir-223 0.1056 −0.1379 Xq12-13.3 mir-023b 0.00964 9q22.1 10 mir-29a-2 0.1139 −0.1487 7q32 mir-155 0.00959 21q21 11 mir-155 −0.1155 0.1508 21q21 mir-223 0.00774 Xq12-13.3 12 mir-221 −0.1157 0.1511 Xp11.3 mir-132 0.00461 17p13.3 13 mir-16-1 −0.1444 0.1886 13q14.3 mir-029a-2 0.00446 7q32 14 mir-16-2 −0.1619 0.2113 3q26.1 mir-024-1 0.00311 9q22.1 15 mir-146 −0.1803 0.2354 5q34 mir-29b-2 (102) 0.000778 1q32.2-32.3 16 mir-29b-2 0.2065 −0.2696 1q32.2-32.3 mir-146 0.000753 5q34 (102) 17 mir-029c 0.2174 −0.2839 1q32.2-32.3 mir-016-1 0.00042 13q14.3 18 mir-016-2 0.000327 3q26.1 19 mir-029c 0.000216 1q32.2-32.3 *the list of genes is in ascending order of significance, as represented by score or p value, respectively.

TABLE 21 Predictions of ZAP-70 status and Immunoglobulin heavy chain variable gene status according to miRNA expression in CLL patients*. CLL True Value Prediction n margin y margin PANEL 1 - CLL01 Zap70 < 20 VhM Zap70 < 20 VhM 1.278 −1.327 83 correct predictions, CLL02 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 0 incorrect predictions. CLL03 Zap70 < 20 VhM Zap70 < 20 VhM 1.247 −1.348 CLL04 Zap70 < 20 VhM Zap70 < 20 VhM 1.16 −1.388 CLL05 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL06 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL07 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1.122 CLL08 Zap70 < 20 VhM Zap70 < 20 VhM 1.391 −1.595 CLL09 Zap70 < 20 VhM Zap70 < 20 VhM 0.953 −1.048 CLL10 Zap70 < 20 VhM Zap70 < 20 VhM 1.059 −1.333 CLL11 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL12 Zap70 < 20 VhM Zap70 < 20 VhM 0.997 −1.261 CLL13 Zap70 < 20 VhM Zap70 < 20 VhM 1.488 −1.841 CLL14 Zap70 < 20 VhM Zap70 < 20 VhM 2.171 −2.582 CLL15 Zap70 < 20 VhM Zap70 < 20 VhM 1.252 −1.352 CLL16 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1.188 CLL17 Zap70 < 20 VhM Zap70 < 20 VhM 1.19 −1.284 CLL18 Zap70 < 20 VhM Zap70 < 20 VhM 1.747 −2.062 CLL19 Zap70 < 20 VhM Zap70 < 20 VhM 1.503 −1.833 CLL20 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL21 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL22 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL23 Zap70 < 20 VhM Zap70 < 20 VhM 2.047 −2.27 CLL24 Zap70 < 20 VhM Zap70 < 20 VhM 1.464 −1.527 CLL25 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL26 Zap70 < 20 VhM Zap70 < 20 VhM 1.034 −1.034 CLL27 Zap70 < 20 VhM Zap70 < 20 VhM 1.479 −1.617 CLL28 Zap70 < 20 VhM Zap70 < 20 VhM 2.355 −2.57 CLL29 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL30 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL31 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL32 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL33 Zap70 < 20 VhM Zap70 < 20 VhM 2.229 −2.496 CLL34 Zap70 < 20 VhM Zap70 < 20 VhM 2.683 −2.931 CLL35 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL36 Zap70 < 20 VhM Zap70 < 20 VhM 2.578 −2.768 CLL37 Zap70 < 20 VhM Zap70 < 20 VhM 2.079 −2.34 CLL38 Zap70 < 20 VhM Zap70 < 20 VhM 1.745 −1.814 CLL39 Zap70 < 20 VhM Zap70 < 20 VhM 1.559 −1.699 CLL40 Zap70 < 20 VhM Zap70 < 20 VhM 2.608 −3.005 CLL41 Zap70 < 20 VhM Zap70 < 20 VhM 2.357 −2.676 CLL42 Zap70 < 20 VhM Zap70 < 20 VhM 1.102 −1.303 CLL43 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL44 Zap70 < 20 VhM Zap70 < 20 VhM 2.464 −2.629 CLL45 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL46 Zap70 < 20 VhM Zap70 < 20 VhM 1 −1 CLL47 Zap70 < 20 VhM Zap70 < 20 VhM 2.074 −2.271 CLL48 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL49 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.179 1.487 CLL50 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 0.88 CLL51 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL52 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.836 2.405 CLL53 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL54 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.334 1.649 CLL55 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1.229 CLL56 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL57 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL58 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.171 1.566 CLL59 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL60 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL61 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.505 1.976 CLL62 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.095 1.46 CLL63 Zap70 > 20 VhUM Zap70 > 20 VhUM −2.297 2.717 CLL64 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.187 1.381 CLL65 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL66 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.344 1.479 CLL67 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.876 2.049 CLL68 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL69 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.89 1.987 CLL70 Zap70 > 20 VhUM Zap70 > 20 VhUM −2.658 2.938 CLL71 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.556 1.967 CLL72 Zap70 > 20 VhUM Zap70 > 20 VhUM −2.574 2.81 CLL73 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL74 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL75 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL76 Zap70 > 20 VhUM Zap70 > 20 VhUM −2.671 3.041 CLL77 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1.376 CLL78 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL79 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.678 1.914 CLL80 Zap70 > 20 VhUM Zap70 > 20 VhUM −2.416 2.953 CLL81 Zap70 > 20 VhUM Zap70 > 20 VhUM −1 1 CLL82 Zap70 > 20 VhUM Zap70 > 20 VhUM −1.782 1.846 CLL83 Zap70 > 20 VhUM Zap70 > 20 VhUM −2.307 2.716 PANEL 2 - CLL95 Zap70 < 20 Zap70 < 20 8.494 −8.494 50 correct predictions, CLL96 Zap70 < 20 Zap70 < 20 1 −1 0 incorrect predictions CLL97 Zap70 < 20 Zap70 < 20 0.763 −0.763 CLL98 Zap70 < 20 Zap70 < 20 11.19 −11.19 CLL99 Zap70 < 20 Zap70 < 20 7.561 −7.561 CLL100 Zap70 < 20 Zap70 < 20 14.51 −14.51 CLL101 Zap70 < 20 Zap70 < 20 5.585 −5.585 CLL102 Zap70 < 20 Zap70 < 20 1 −1 CLL103 Zap70 < 20 Zap70 < 20 10.09 −10.09 CLL104 Zap70 < 20 Zap70 < 20 5.521 −5.521 CLL105 Zap70 < 20 Zap70 < 20 7.33 −7.33 CLL106 Zap70 < 20 Zap70 < 20 3.264 −3.264 CLL107 Zap70 < 20 Zap70 < 20 7.774 −7.774 CLL108 Zap70 < 20 Zap70 < 20 5.3 −5.3 CLL109 Zap70 < 20 Zap70 < 20 4.34 −4.34 CLL110 Zap70 < 20 Zap70 < 20 1.822 −1.822 CLL111 Zap70 < 20 Zap70 < 20 3.879 −3.879 CLL112 Zap70 < 20 Zap70 < 20 8.514 −8.514 CLL113 Zap70 < 20 Zap70 < 20 5.866 −5.866 CLL114 Zap70 < 20 Zap70 < 20 10.69 −10.69 CLL115 Zap70 < 20 Zap70 < 20 4.141 −4.141 CLL116 Zap70 < 20 Zap70 < 20 1 −1 CLL117 Zap70 < 20 Zap70 < 20 1 −1 CLL118 Zap70 < 20 Zap70 < 20 1 −1 CLL119 Zap70 < 20 Zap70 < 20 10.11 −10.11 CLL120 Zap70 > 20 Zap70 > 20 −3.109 3.109 CLL121 Zap70 > 20 Zap70 > 20 −4.722 4.722 CLL122 Zap70 > 20 Zap70 > 20 −5.166 5.166 CLL123 Zap70 > 20 Zap70 > 20 −7.828 7.828 CLL124 Zap70 > 20 Zap70 > 20 −7.468 7.468 CLL125 Zap70 > 20 Zap70 > 20 −11.44 11.44 CLL126 Zap70 > 20 Zap70 > 20 −1 1 CLL127 Zap70 > 20 Zap70 > 20 −6.617 6.617 CLL128 Zap70 > 20 Zap70 > 20 −7.011 7.011 CLL129 Zap70 > 20 Zap70 > 20 −7.479 7.479 CLL130 Zap70 > 20 Zap70 > 20 −9.568 9.568 CLL131 Zap70 > 20 Zap70 > 20 −5.286 5.286 CLL132 Zap70 > 20 Zap70 > 20 −5.045 5.045 CLL133 Zap70 > 20 Zap70 > 20 −1 1 CLL134 Zap70 > 20 Zap70 > 20 −1 1 CLL135 Zap70 > 20 Zap70 > 20 −1.324 1.324 CLL136 Zap70 > 20 Zap70 > 20 −1 1 CLL137 Zap70 > 20 Zap70 > 20 −1 1 CLL138 Zap70 > 20 Zap70 > 20 −9.649 9.649 CLL139 Zap70 > 20 Zap70 > 20 −9.264 9.264 CLL140 Zap70 > 20 Zap70 > 20 −7.13 7.13 CLL141 Zap70 > 20 Zap70 > 20 −11.77 11.77 CLL142 Zap70 > 20 Zap70 > 20 −2.986 2.986 CLL143 Zap70 > 20 Zap70 > 20 −1 1 CLL144 Zap70 > 20 Zap70 > 20 −1 1 *Prediction for 83 CLLs, from groups 1 and 4 (see text). Classification was generated by the ‘Support Vector Machines’ algorithm (Kernel Function used: Polynomial Dot Product (Order 2). Diagonal Scaling Factor: 0). The miRNA signature associated with prognostic factors was generated using panel 1 samples and then tested to cross validate the panel 1 and to predict the status of samples from panel 2. Association Between miRNA Expression and Time to Initial Therapy.

This analysis was performed as described in Example 12. All of the microRNAs which can predict the time to initial therapy, with the exception of mir-29c, are overexpressed in the group characterized by a short interval from diagnosis to initial therapy (Table 22). The PAM score for each of the components of microRNA signature associated with the time from diagnosis to initial therapy is presented in Table 23.

TABLE 22 Relative expression levels of microRNAs predictive of the time interval from diagnosis to initial therapy. Short Long interval interval microarray expression hsa-mir-181a High Low hsa-mir-155 High Low hsa-mir-146 High Low hsa-mir-024-2 High Low hsa-mir-023b High Low hsa-mir-023a High Low hsa-mir-222 High Low hsa-mir-221 High Low hsa-mir-029c Low High

TABLE 23 PAM score for each of the components of microRNA signature associated with the time from diagnosis to initial therapy. 1 score 2 score hsa-mir-181a 0.1862 −0.0603 hsa-mir-155 0.1409 −0.0456 hsa-mir-146 0.07 −0.0227 hsa-mir-024-2 0.0696 −0.0225 hsa-mir-023b 0.0643 −0.0208 hsa-mir-023a 0.0587 −0.019 hsa-mir-222 0.0458 −0.0148 hsa-mir-221 0.0343 −0.0111 hsa-mir-029c −0.0221 0.0072 Note: Score 1 characterize the short time; score 2 the long time from diagnosis to initial therapy in a panel of 94 CLL patients.

The relevant teachings of all publications cited herein that have not explicitly been incorporated by reference, are incorporated herein by reference in their entirety. One skilled in the art will readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The present invention may be embodied in other specific forms without departing from the spirit or essential attributes thereof and, accordingly, reference should be made to the appended claims, rather than to the foregoing specification, as indicating the scope of the invention. 

1. A method of determining increased risk of a human subject developing a cancer, or increased likelihood of the presence of a cancer in a human subject, comprising the steps of: (i) measuring in a sample from the subject the level of at least one miR-155(BIC) gene product; and (ii) comparing the level of the at least one miR-155(BIC) gene product in the sample to a control level of the miR-155(BIC) gene product, wherein an increase in the level of the miR-155(BIC) gene product in the sample relative to the control level of miR-155(BIC) gene product is indicative of the subject either having increased risk of developing the cancer or increased likelihood of the presence of the cancer.
 2. The method of claim 1, wherein the at least one miR-155(BIC) gene product comprises SEQ ID NO:183.
 3. The method of claim 1, wherein the at least one miR-155(BIC) gene product comprises nucleotides 4-25 of SEQ ID NO:183.
 4. The method of claim 1, wherein the cancer is selected from the group consisting of: bladder cancer; esophageal cancer; lung cancer; stomach cancer; kidney cancer; cervical cancer; ovarian cancer; breast cancer; lymphoma; Ewing sarcoma; hematopoietic tumors; solid tumors; gastric cancer; colorectal cancer; brain cancer; epithelial cancer; nasopharyngeal cancer; uterine cancer; hepatic cancer; head-and-neck cancer; renal cancer; male germ cell tumors; malignant mesothelioma; myelodysplastic syndrome; pancreatic or biliary cancer; prostate cancer; thyroid cancer; urothelial cancer; renal cancer; Wilm's tumor; small cell lung cancer; melanoma; skin cancer; osteosarcoma; neuroblastoma; leukemia (acute lymphocytic leukemia, acute myeloid leukemia, chronic lymphocytic leukemia); glioblastoma multiforme; medulloblastoma; lymphoplasmacytoid lymphoma; and rhabdomyosarcoma.
 5. The method of claim 4, wherein the cancer is breast cancer.
 6. The method of claim 4, wherein the cancer is lung cancer.
 7. The method of claim 6, wherein the lung cancer is small cell lung cancer.
 8. The method of claim 4, wherein the cancer is colorectal cancer.
 9. The method of claim 1, wherein the level of the at least one miR-155(BIC) gene product in the sample is measured using an assay selected from the group consisting of northern blot analysis, in situ hybridization and quantitative reverse transcriptase polymerase chain reaction.
 10. The method of claim 1, wherein the sample is a tissue sample.
 11. The method of claim 10, wherein the tissue sample is a biopsy.
 12. The method of claim 1, wherein the sample is a blood sample.
 13. A method of determining increased risk of a human subject developing a cancer, or increased likelihood of the presence of a cancer in a human subject, comprising the steps of: (1) reverse transcribing at least one miR-155(BIC) RNA from a sample from the subject to provide at least one miR-155(BIC) target oligodeoxynucleotide; (2) hybridizing the at least one miR-155(BIC) target oligodeoxynucleotide to a microarray comprising miRNA-specific probe oligonucleotides that include at least one miR-155(BIC) RNA-specific probe oligonucleotide to provide a hybridization profile for the sample, wherein the hybridization profile includes a hybridization signal for the at least one miR-155(BIC) RNA; and (3) comparing the sample hybridization profile to a control hybridization profile, wherein the control hybridization profile includes a control hybridization signal for the at least one miR-155(BIC) RNA, wherein a hybridization signal for the at least one miR-155(BIC) RNA in the sample hybridization profile that is greater than the control hybridization signal for the at least one miR-155(BIC) RNA indicates the subject has increased risk of developing the cancer or increased likelihood of the presence of the cancer.
 14. The method of claim 13, wherein the at least one miR-155(BIC) gene product comprises SEQ ID NO:183.
 15. The method of claim 13, wherein the at least one miR-155(BIC) gene product comprises nucleotides 4-25 of SEQ ID NO:183.
 16. The method of claim 13, wherein the cancer is selected from the group consisting of: bladder cancer; esophageal cancer; lung cancer; stomach cancer; kidney cancer; cervical cancer; ovarian cancer; breast cancer; lymphoma; Ewing sarcoma; hematopoietic tumors; solid tumors; gastric cancer; colorectal cancer; brain cancer; epithelial cancer; nasopharyngeal cancer; uterine cancer; hepatic cancer; head-and-neck cancer; renal cancer; male germ cell tumors; malignant mesothelioma; myelodysplastic syndrome; pancreatic or biliary cancer; prostate cancer; thyroid cancer; urothelial cancer; renal cancer; Wilm's tumor; small cell lung cancer; melanoma; skin cancer; osteosarcoma; neuroblastoma; leukemia (acute lymphocytic leukemia, acute myeloid leukemia, chronic lymphocytic leukemia); glioblastoma multiforme; medulloblastoma; lymphoplasmacytoid lymphoma; and rhabdomyosarcoma.
 17. The method of claim 16, wherein the cancer is selected from the group consisting of: breast cancer; lung cancer; and colorectal cancer.
 18. The method of claim 13, wherein the sample is a tissue sample.
 19. The method of claim 13, wherein the sample is a blood sample.
 20. The method of claim 13, wherein the microarray comprises miRNA-specific probes oligonucleotides for a substantial portion of the human miRNome. 